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As of 1-Dec-2021 number of released structures: 11785
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 8063  Download results as an excel file       Gallery view

NDB ID:

 7KST

PDB ID:

7KST 

Release:

2021-12-01

Title:

DNA Polymerase Mu, dGTP:Ct Reaction State Ternary Complex, 10 mM Mn2+ (2min)

Classification:

REPLICATION/DNA

Authors:

Jamsen, J.A., Sassa, A., Shock, D.D., Beard, W.A., Wilson, S.H.

Citation:

DNA Polymerase Mu, dGTP:Ct Reaction State Ternary Complex, 10 mM Mn2+ (2min)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.599Å R work:0.163R free:0.185

NDB ID:

 7KSV

PDB ID:

7KSV 

Release:

2021-12-01

Title:

DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mn2+ (960min)

Classification:

REPLICATION/DNA

Authors:

Jamsen, J.A., Sassa, A., Shock, D.D., Beard, W.A., Wilson, S.H.

Citation:

DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mn2+ (960min)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.64Å R work:0.162R free:0.187

NDB ID:

 7KSW

PDB ID:

7KSW 

Release:

2021-12-01

Title:

DNA Polymerase Mu, dGTP:Ct Reaction State Ternary Complex, 10 mM Mg2+ (10min)

Classification:

REPLICATION/DNA

Authors:

Jamsen, J.A., Sassa, A., Shock, D.D., Beard, W.A., Wilson, S.H.

Citation:

DNA Polymerase Mu, dGTP:Ct Reaction State Ternary Complex, 10 mM Mg2+ (10min)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.49Å R work:0.154R free:0.171

NDB ID:

 7KSX

PDB ID:

7KSX 

Release:

2021-12-01

Title:

DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mg2+ (30min)

Classification:

REPLICATION/DNA

Authors:

Jamsen, J.A., Sassa, A., Shock, D.D., Beard, W.A., Wilson, S.H.

Citation:

DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mg2+ (30min)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.57Å R work:0.163R free:0.186

NDB ID:

 7KSY

PDB ID:

7KSY 

Release:

2021-12-01

Title:

DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mg2+ (960min)

Classification:

REPLICATION/DNA

Authors:

Jamsen, J.A., Sassa, A., Shock, D.D., Beard, W.A., Wilson, S.H.

Citation:

DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mg2+ (960min)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.577Å R work:0.155R free:0.169

NDB ID:

 7KU4

PDB ID:

7KU4 

Release:

2021-12-01

Title:

DNA-DB818 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents a binding site for the heterocyclic small molecule (DB818).

Classification:

DNA

Authors:

Ogbonna, E., Fang, Z., Wilson, W.D.

Citation:

DNA-DB818 complex
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.6Å R work:0.216R free:0.23

NDB ID:

 7NX5

PDB ID:

7NX5 

Release:

2021-12-01

Title:

Crystal structure of the Epstein-Barr Virus protein ZEBRA (BZLF1, Zta) bound to a methylated DNA duplex

Classification:

VIRAL PROTEIN

Authors:

Bernaudat, F., Gustems, M., Guenther, J., Oliva, M.F., Buschle, A., Goebel, C., Pagniez, P., Lupo, J., Signor, L., Mueller, C.W., Morand, P., Sattler, M., Hammerschmidt, W., Petosa, C.

Citation:

Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.276R free:0.338

NDB ID:

 7QB3

PDB ID:

7QB3 

Release:

2021-12-01

Title:

Solution structure of a lanthanide-binding DNA aptamer

Classification:

DNA

Authors:

Andralojc, W., Pasternak, K., Wieruszewska, J., Gdaniec, Z.

Citation:

Solution structure of a lanthanide-binding DNA aptamer
To Be Published pp. - 0

Experiment:

 SOLUTION NMR

NDB ID:

 7VUP

PDB ID:

7VUP 

Release:

2021-11-24

Title:

Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Meshcheryakov, V.A., Wang, V.Y.-F.

Citation:

Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.4Å R work:0.271R free:0.285

NDB ID:

 7VUQ

PDB ID:

7VUQ 

Release:

2021-11-24

Title:

Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Meshcheryakov, V.A., Wang, V.Y.-F.

Citation:

Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.224R free:0.248

NDB ID:

 7KII

PDB ID:

7KII 

Release:

2021-11-17

Title:

Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+

Classification:

REPLICATION/DNA

Authors:

Tompkins, K.

Citation:

Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+
to be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.3Å R work:0.149R free:0.184

NDB ID:

 7KIJ

PDB ID:

7KIJ 

Release:

2021-11-17

Title:

Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site

Classification:

REPLICATION/DNA

Authors:

Tompkins, K.

Citation:

Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
to be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.69Å R work:0.17R free:0.194

NDB ID:

 7KIK

PDB ID:

7KIK 

Release:

2021-11-17

Title:

Wheat dwarf virus Rep domain circular permutation complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+

Classification:

REPLICATION/DNA

Authors:

Tompkins, K.

Citation:

Wheat dwarf virus Rep domain circular permutation complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+
to be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.73Å R work:0.155R free:0.187

NDB ID:

 7LXH

PDB ID:

7LXH 

Release:

2021-11-17

Title:

Bacillus cereus DNA glycosylase AlkD bound to a CC1065-adenine nucleobase adduct and DNA containing an abasic site

Classification:

HYDROLASE/DNA/ANTIBIOTIC

Authors:

Mullins, E.A., Dorival, J., Tang, G.L., Boger, D.L., Eichman, B.F.

Citation:

Structural evolution of a DNA repair self-resistance mechanism targeting duocarmycin family secondary metabolites
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.667Å R work:0.148R free:0.182

NDB ID:

 7LXJ

PDB ID:

7LXJ 

Release:

2021-11-17

Title:

Bacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-adenine nucleobase adduct and DNA containing an abasic site

Classification:

HYDROLASE/DNA/ANTIBIOTIC

Authors:

Mullins, E.A., Dorival, J., Tang, G.L., Boger, D.L., Eichman, B.F.

Citation:

Structural evolution of a DNA repair self-resistance mechanism targeting duocarmycin family secondary metabolites
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.93Å R work:0.153R free:0.201

NDB ID:

 7BHY

PDB ID:

7BHY 

Release:

2021-11-10

Title:

DNA-binding domain of DeoR in complex with the DNA operator

Classification:

DNA BINDING PROTEIN

Authors:

Soltysova, M., Sieglova, I., Fabry, M., Brynda, J., Skerlova, J., Rezacova, P.

Citation:

Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family.
Acta Crystallogr D Struct Biol 77 pp.1411 - 1424 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.3Å R work:0.206R free:0.263

NDB ID:

 7BI0

PDB ID:

7BI0 

Release:

2021-11-10

Title:

GA repetition with i-motif clip at 5'-end

Classification:

DNA

Authors:

Novotny, A., Novotny, J., Kejnovska, I., Vorlickova, M., Fiala, R., Marek, R.

Citation:

Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip.
Nucleic Acids Res. 49 pp.11425 - 11437 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7BL0

PDB ID:

7BL0 

Release:

2021-11-10

Title:

GA attached to an i-motif clip at 3'-end

Classification:

DNA

Authors:

Novotny, A., Novotny, J., Kejnovska, I., Vorlickova, M., Fiala, R., Marek, R.

Citation:

Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip.
Nucleic Acids Res. 49 pp.11425 - 11437 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7BLM

PDB ID:

7BLM 

Release:

2021-11-10

Title:

AG repetition attached to a compact i-motif clip at 3'-end

Classification:

DNA

Authors:

Novotny, A., Novotny, J., Kejnovska, I., Vorlickova, M., Fiala, R., Marek, R.

Citation:

Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip.
Nucleic Acids Res. 49 pp.11425 - 11437 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7BMA

PDB ID:

7BMA 

Release:

2021-11-10

Title:

AG repetition attached to an extended i-motif clip at 3'-end

Classification:

DNA

Authors:

Novotny, A., Novotny, J., Kejnovska, I., Vorlickova, M., Fiala, R., Marek, R.

Citation:

Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip.
Nucleic Acids Res. 49 pp.11425 - 11437 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7KZ0

PDB ID:

7KZ0 

Release:

2021-11-10

Title:

Human MBD4 glycosylase domain bound to DNA containing substrate analog 2'-deoxy-pseudouridine

Classification:

HYDROLASE/DNA

Authors:

Pidugu, L.S., Bright, H., Lin, W.J., Majumdar, C., Van Ostrand, R.P., David, S.S., Pozharski, E., Drohat, A.C.

Citation:

Structural Insights into the Mechanism of Base Excision by MBD4.
J.Mol.Biol. 433 pp.167097 - 167097 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.57Å R work:0.188R free:0.215

NDB ID:

 7KZ1

PDB ID:

7KZ1 

Release:

2021-11-10

Title:

Human MBD4 glycosylase domain bound to DNA containing an abasic site

Classification:

HYDROLASE/DNA

Authors:

Pidugu, L.S., Bright, H., Lin, W.J., Majumdar, C., Van Ostrand, R.P., David, S.S., Pozharski, E., Drohat, A.C.

Citation:

Structural Insights into the Mechanism of Base Excision by MBD4.
J.Mol.Biol. 433 pp.167097 - 167097 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.62Å R work:0.181R free:0.205

NDB ID:

 7KZG

PDB ID:

7KZG 

Release:

2021-11-10

Title:

Human MBD4 glycosylase domain bound to DNA containing oxacarbenium-ion analog 1-aza-2'-deoxyribose

Classification:

HYDROLASE/DNA

Authors:

Pidugu, L.S., Bright, H., Lin, W.J., Majumdar, C., Van Ostrand, R.P., David, S.S., Pozharski, E., Drohat, A.C.

Citation:

Structural Insights into the Mechanism of Base Excision by MBD4.
J.Mol.Biol. 433 pp.167097 - 167097 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.68Å R work:0.168R free:0.204

NDB ID:

 7OYK

PDB ID:

7OYK 

Release:

2021-11-10

Title:

DNA-binding domain of CggR in complex with the DNA operator

Classification:

DNA BINDING PROTEIN

Authors:

Soltysova, M., Sieglova, I., Fabry, M., Brynda, J., Skerlova, J., Rezacova, P.

Citation:

Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family.
Acta Crystallogr D Struct Biol 77 pp.1411 - 1424 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.101Å R work:0.208R free:0.252

NDB ID:

 7SOZ

PDB ID:

7SOZ 

Release:

2021-11-10

Title:

Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (5 mg/mL EDC, 12 hours).

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Ward, A.R., Dmytriw, S., Vajapayajula, A., Snow, C.D.

Citation:

Stabilizing DNA-protein co-crystals via in crystallo chemical ligation of the DNA
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.14Å R work:0.193R free:0.263

NDB ID:

 7SPM

PDB ID:

7SPM 

Release:

2021-11-10

Title:

Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (30 mg/mL EDC, 12 hours, 2 doses).

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Ward, A.R., Dmytriw, S., Vajapayajula, A., Snow, C.D.

Citation:

Stabilizing DNA-protein co-crystals via in crystallo chemical ligation of the DNA
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.28Å R work:0.2R free:0.252

NDB ID:

 7DW5

PDB ID:

7DW5 

Release:

2021-11-03

Title:

Crystal structure of DUX4 HD1-HD2 domain complexed with ERG sites

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Zhang, H., Cheng, N., Li, Z., Bai, L., Fang, C., Li, Y., Zhang, W., Dong, X., Jiang, M., Liang, Y., Zhang, S., Mi, J., Zhu, J., Zhang, Y., Chen, S.J., Zhao, Y., Weng, X.Q., Hu, W., Chen, Z., Huang, J., Meng, G.

Citation:

DNA crosslinking and recombination-activating genes 1/2 (RAG1/2) are required for oncogenic splicing in acute lymphoblastic leukemia.
Cancer Commun (Lond) pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.83Å R work:0.222R free:0.241

NDB ID:

 7KLE

PDB ID:

7KLE 

Release:

2021-11-03

Title:

Ternary structure of Dpo4 bound to N7mG in the template base paired with incoming dCTP

Classification:

DNA BINDING PROTEIN

Authors:

Koag, M.-C., Lee, S.

Citation:

Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.003Å R work:0.229R free:0.287

NDB ID:

 7KLF

PDB ID:

7KLF 

Release:

2021-11-03

Title:

Ternary structure of Dpo4 bound to G in the template base paired with incoming dCTP

Classification:

DNA BINDING PROTEIN

Authors:

Koag, M.-C., Lee, S.

Citation:

Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.301Å R work:0.231R free:0.279

NDB ID:

 7L4V

PDB ID:

7L4V 

Release:

2021-11-03

Title:

C-terminal bZIP domain of human C/EBPbeta Bound to DNA with Consensus Recognition with GT Mismatch

Classification:

TRANSCRIPTION/DNA

Authors:

Yang, J., Horton, J.R., Akdemir, K.C., Li, J., Huang, Y., Kumar, J., Blumenthal, R.M., Zhang, X., Cheng, X.

Citation:

Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations.
Nucleic Acids Res. 49 pp.5084 - 5094 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.75Å R work:0.199R free:0.221

NDB ID:

 7L4X

PDB ID:

7L4X 

Release:

2021-11-03

Title:

YTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA joined by two six-bp DNA duplexes in P3221 Crystal

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Yu, D., Horton, J.R., Yang, J., Hajian, T., Vedadi, M., Sagum, C.A., Bedford, M.T., Blumenthal, R.M., Zhang, X., Cheng, X.

Citation:

Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions.
Nucleic Acids Res. 49 pp.11629 - 11642 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.79Å R work:0.198R free:0.231

NDB ID:

 7L4Y

PDB ID:

7L4Y 

Release:

2021-11-03

Title:

YTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA joined by Two Six-bp DNA Duplexes in P212121 Crystal

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Yu, D., Horton, J.R., Yang, J., Hajian, T., Vedadi, M., Sagum, C.A., Bedford, M.T., Blumenthal, R.M., Zhang, X., Cheng, X.

Citation:

Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions.
Nucleic Acids Res. 49 pp.11629 - 11642 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.79Å R work:0.207R free:0.239

NDB ID:

 7MK1

PDB ID:

7MK1 

Release:

2021-11-03

Title:

Structure of a protein-modified aptamer complex

Classification:

IMMUNE SYSTEM/DNA

Authors:

Ren, X., Gelinas, A.D., Linehan, M., Iwasaki, A., Wang, W., Janjic, N., Pyle, A.M.

Citation:

Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA.
J.Mol.Biol. 433 pp.167227 - 167227 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.188R free:0.219

NDB ID:

 7N7D

PDB ID:

7N7D 

Release:

2021-11-03

Title:

Solution structure of the MYC promoter G-quadruplex in complex with berberine: conformer A

Classification:

DNA

Authors:

Dickerhoff, J., Brundridge, N., McLuckey, S.A., Yang, D.

Citation:

Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution.
J.Med.Chem. 64 pp.16205 - 16212 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7N7E

PDB ID:

7N7E 

Release:

2021-11-03

Title:

Solution structure of the MYC promoter G-quadruplex in complex with berberine: conformer B

Classification:

DNA

Authors:

Dickerhoff, J., Brundridge, N., McLuckey, S.A., Yang, D.

Citation:

Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution.
J.Med.Chem. 64 pp.16205 - 16212 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7OGV

PDB ID:

7OGV 

Release:

2021-11-03

Title:

A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine

Classification:

DNA

Authors:

Battistini, F., Dans, P.D., Terrazas, M., Castellazzi, C.L., Portella, G., Labrador, M., Villegas, N., Brun-Heath, I., Gonzalez, C., Orozco, M.

Citation:

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.
Plos Comput.Biol. 17 pp.e1009547 - e1009547 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7OHE

PDB ID:

7OHE 

Release:

2021-11-03

Title:

A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine

Classification:

DNA

Authors:

Battistini, F., Dans, P.D., Terrazas, M., Castellazzi, C.L., Portella, G., Labrador, M., Villegas, N., Brun-Heath, I., Gonzalez, C., Orozco, M.

Citation:

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.
Plos Comput.Biol. 17 pp.e1009547 - e1009547 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7OHJ

PDB ID:

7OHJ 

Release:

2021-11-03

Title:

A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine

Classification:

DNA

Authors:

Battistini, F., Dans, P.D., Terrazas, M., Castellazzi, C.L., Portella, G., Labrador, M., Villegas, N., Brun-Heath, I., Gonzalez, C., Orozco, M.

Citation:

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.
Plos Comput.Biol. 17 pp.e1009547 - e1009547 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7OHM

PDB ID:

7OHM 

Release:

2021-11-03

Title:

A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine

Classification:

DNA

Authors:

Battistini, F., Dans, P.D., Terrazas, M., Castellazzi, C.L., Portella, G., Labrador, M., Villegas, N., Brun-Heath, I., Gonzalez, C., Orozco, M.

Citation:

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.
Plos Comput.Biol. 17 pp.e1009547 - e1009547 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7RSU

PDB ID:

7RSU 

Release:

2021-10-27

Title:

TNA polymerase, n+2 product

Classification:

TRANSFERASE/DNA

Authors:

Li, Q., Maola, V.A., Chim, N., Hussain, J., Lozoya-Colinas, A., Chaput, J.C.

Citation:

Synthesis and Polymerase Recognition of Threose Nucleic Acid Triphosphates Equipped with Diverse Chemical Functionalities.
J.Am.Chem.Soc. 143 pp.17761 - 17768 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.181R free:0.231

NDB ID:

 7MSV

PDB ID:

7MSV 

Release:

2021-10-20

Title:

Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter

Classification:

DNA

Authors:

Wang, K.B., Dickerhoff, J., Yang, D.

Citation:

Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-beta Promoter.
J.Am.Chem.Soc. 143 pp.16549 - 16555 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7MVS

PDB ID:

7MVS 

Release:

2021-10-20

Title:

DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution

Classification:

ISOMERASE/DNA/ANTIBIOTIC

Authors:

Lu, Y., Vibhute, S., Li, L., Okumu, A., Ratigan, S.C., Nolan, S., Papa, J.L., Mann, C.A., English, A., Chen, A., Seffernick, J.T., Koci, B., Duncan, L.R., Roth, B., Cummings, J.E., Slayden, R.A., Lindert, S., McElroy, C.A., Wozniak, D.J., Yalowich, J., Mitton-Fry, M.J.

Citation:

Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA.
J.Med.Chem. 64 pp.15214 - 15249 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.60137Å R work:0.195R free:0.251

NDB ID:

 7R96

PDB ID:

7R96 

Release:

2021-10-20

Title:

Self-Assembled 3D DNA Hexagonal Tensegrity Triangle

Classification:

DNA

Authors:

Lu, B., Vecchioni, S., Ohayon, Y.P., Sha, R., Woloszyn, K., Yang, B., Mao, C., Seeman, N.C.

Citation:

3D Hexagonal Arrangement of DNA Tensegrity Triangles.
Acs Nano 15 pp.16788 - 16793 2021

Experiment:

 X-RAY DIFFRACTION Resolution:5.68Å R work:0.119R free:0.143

NDB ID:

 7VJQ

PDB ID:

7VJQ 

Release:

2021-10-20

Title:

Pectobacterium phage ZF40 apo-aca2 complexed with 26bp DNA substrate

Classification:

TRANSCRIPTION/DNA

Authors:

Liu, Y.H., Zhang, L.S., Wu, B.X., Huang, H.D.

Citation:

Pectobacterium phage ZF40 apo-aca2
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.79Å R work:0.19R free:0.218

NDB ID:

 7D8T

PDB ID:

7D8T 

Release:

2021-10-13

Title:

MITF bHLHLZ complex with M-box DNA

Classification:

TRANSCRIPTION/DNA

Authors:

Liu, Z., Chen, K., Yu, J., Liang, Y., Zhao, Z., Bennet, S., Xu, P., Park, C., Fallahi, M., Dai, J., Feng, Y., Chase, P., Spicer, T., Pan, L., Fang, P., Yu, B., Wang, J., Guo, M., Fisher, D., Wang, J.

Citation:

Targeting the Lineage-specific Dynamic Microphthalmia-Associated Transcription Factor (MITF) for melanoma treatment
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.201Å R work:0.203R free:0.234

NDB ID:

 7F2F

PDB ID:

7F2F 

Release:

2021-10-13

Title:

The complex of DNA with the C-terminal domain of TYE7 from Saccharomyces cerevisiae.

Classification:

TRANSCRIPTION

Authors:

Gui, W., Xue, L., Yue, J., Kuang, Z., Jin, Y., Niu, L.

Citation:

Crystal structure of the complex of DNA with the C-terminal domain of TYE7 from Saccharomyces cerevisiae.
Acta Crystallogr.,Sect.F 77 pp.341 - 347 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.55Å R work:0.245R free:0.283

NDB ID:

 7N8S

PDB ID:

7N8S 

Release:

2021-10-13

Title:

LINE-1 endonuclease domain complex with DNA

Classification:

HYDROLASE/DNA

Authors:

Miller, I., Totrov, M., Korotchkina, L., Kazyulkin, D.N., Gudkov, A.V., Korolev, S.

Citation:

Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.
Nucleic Acids Res. 49 pp.11350 - 11366 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.79Å R work:0.263R free:0.321

NDB ID:

 7N94

PDB ID:

7N94 

Release:

2021-10-13

Title:

LINE-1 endonuclease domain complex with DNA

Classification:

HYDROLASE/DNA

Authors:

Miller, I., Totrov, M., Korotchkina, L., Kazyulkin, D.N., Gudkov, A.V., Korolev, S.

Citation:

Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.
Nucleic Acids Res. 49 pp.11350 - 11366 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.85Å R work:0.214R free:0.28

NDB ID:

 7OM3

PDB ID:

7OM3 

Release:

2021-10-13

Title:

Crystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine containing template

Classification:

REPLICATION

Authors:

Kropp, H.M., Ludmann, S., Diederichs, K., Betz, K., Marx, A.

Citation:

Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase.
Chembiochem 22 pp.3060 - 3066 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.92Å R work:0.182R free:0.233

NDB ID:

 7OMB

PDB ID:

7OMB 

Release:

2021-10-13

Title:

Crystal structure of KOD DNA Polymerase in a ternary complex with a p/t duplex containing an extended 5' single stranded template overhang

Classification:

REPLICATION

Authors:

Kropp, H.M., Ludmann, S., Diederichs, K., Betz, K., Marx, A.

Citation:

Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase.
Chembiochem 22 pp.3060 - 3066 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.01Å R work:0.2R free:0.236

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