MolNFT v1 · #25950 · protein
DNA polymerase from bacteriophage RB69
1WAF: “DNA polymerase from bacteriophage RB69”. X-ray diffraction, 1 ligand (GMP), 20 pockets (best druggability 0.81). MolNFT v1 #25950 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1WAF
- Type
- protein
- Length
- 1,806 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- GMP
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase (EC 2.7.7.7) | protein | 903 | 41% helix, 16% strand | Q38087 |
Ligands and binding sites
- GMP · Guanosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.81 | 0.83 | 101 | empty |
| 2 | 1019 | 0.78 | 0.80 | 83 | empty |
| 3 | 1059 | 0.77 | 0.79 | 77 | empty |
| 4 | 73 | 0.74 | 0.97 | 20 | empty |
| 5 | 55 | 0.73 | 0.98 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1180 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1WAF · DNA polymerase from bacteriophage RB69 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q38087
- Elsewhere: RCSB PDB 1WAF · PDBe 1WAF · UniProt Q38087
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