NDB Search Term Glossary

Summary Search

NDB ID	NDB Identifier (e.g. ADDB01, BDL001)
PDB ID	PDB Identifier (e.g. 1BNA)
Keywords	Relevant keywords (e.g. VIRAL COAT PROTEIN)
Author	Name of primary citation author (e.g. R.E. DICKERSON)

Citation

Year	Year of publication (e.g. 1988)
Released Since	Released since the given date (e.g. 2003-01-01)

Biomolecule Contains

DNA	All structures with DNA strands (Y or N)
RNA	All structures with RNA strands (Y or N)
Hybrid	All structures with both DNA and RNA strands (Y or N)
Protein	All structures with protein chains (Y or N)
Ligand	All small organic molecules and ions (excluding solvents) within the PDB entry
Drug	Ligands which bind to Nucleic Acid molecules with defined binding types (e.g. MAJOR GROOVE BINDER, COVALENT)

Experimental Type

Crystal Structure	Was the structure determined by X-ray crystallography? (Y or N)
Structure Factors Available	Are structure factors deposited in NDB? (Y or N)
NMR	Was the structure determined by NMR spectroscopy? (Y or N)
NMR Restraints Available	Are NMR restraints deposited in NDB? (Y or N)

Nucleic Acid Modifications

Base	Does nucleic acid have base modifiers? (Y or N)
Sugar	Does nucleic acid have sugar modifiers? (Y or N)
Phosphate	Does nucleic acid have phosphate modifiers? (Y or N)

Nucleic Acid Structural Conformational Type

Strand Description	Overall description of NUCLEIC ACID part of biological unit (including protein/NA complexes) (e.g. DOUBLE HELIX, TRIPLE HELIX, QUADRUPLE HELIX, SINGLE STRAND)
Conformation Type	Conformation type of NUCLEIC ACID part of structure (including protein/NA complexes) (e.g. A, B, Z, U (= Unusual), RH (= Right Handed))
Nucleic Acid Features	Special structural features of NUCLEIC ACID part of biological unit (including protein/NA complexes) (e.g. LOOP, BULGE, OVERHANGING BASE)

Protein Binding Mode

Enzyme	Type of enzyme function (e.g. DNA NUCLEASE/ENDONUCLEASE, DNA NUCLEASE/EXONUCLEASE, DNA POLYMERASE, GLYCOSYLASE)
Regulatory	Type of regulatory function (e.g. REPLICATION FACTOR, DNA REPAIR ACTIVATOR, REPLICATION FACTOR/REPRESSOR)
Structural	Type of structural function (e.g. SPLICOSOME COMPONENT, TELOMERE BINDING, VIRAL COAT)
Other	Type of non classified function (e.g. ANTIBODY, THROMBIN)

Experimental Details

Space Group	Space Group (e.g. P 21 21 21, C 2, P 2)
Unit Cell Dimensions	Cell constants a, b, and c; cell angles alpha, beta, and gamma
Resolution	Resolution used in structure refinement
R-factor	The observed R value

Sequence

Nucleic Acid Sequence Pattern	Sequence of residues in the strand (e.g. CGCGUA or (DA)(DA)(DT)(DG) for DNA (using captial letters and NO spaces), Standard NA residues (A, T, C, G, U, I) or Proteins (ALA PRO GLN GLU etc.))