MolNFT v1 · #19110 · protein + DNA
Crystal structure of enterobacteria phage RB69 GP43 DNA polymerase complexed with 8-oxoguanosine containing DNA
1Q9Y · 5'-AC(8-OXOGUANOSINE)GGTAAGCAGTCCGCG-3': “Crystal structure of enterobacteria phage RB69 GP43 DNA polymerase complexed with 8-oxoguanosine containing…”. X-ray diffraction, 2 ligands (DCP, CA), 10 pockets (best druggability 0.84).…
- PDB
- 1Q9Y
- Type
- protein + DNA
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-AC(8-OXOGUANOSINE)GGTAAGCAGTCCGCG-3'; 5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3'; DNA…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DCP, CA
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-AC(8-OXOGUANOSINE)GGTAAGCAGTCCGCG-3' | dna | 18 | — | — |
| P | 5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3' | dna | 14 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 902 | 44% helix, 17% strand | Q38087 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains T, P, A
- CA · Calcium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.84 | 0.95 | 29 | empty |
| 2 | 939 | 0.79 | 0.81 | 81 | empty |
| 3 | 962 | 0.77 | 0.80 | 74 | DCP, CA |
| 4 | 535 | 0.63 | 0.75 | 45 | empty |
| 5 | 110 | 0.55 | 0.83 | 18 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1129 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–A · 716 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 632 Ų buried · 69 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1Q9Y · Crystal structure of enterobacteria phage RB69 GP43 DNA polymerase complexed with… · the same entry in another collection · chain T against T, 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 1Q9Y · PDBe 1Q9Y · UniProt Q38087
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