MolNFT v1 · #76252 · protein + DNA
RB69 DNA polymerase (L561A/S565G/Y567A) ternary complex with dgtp opposite dt
3QEX: “RB69 DNA polymerase (L561A/S565G/Y567A) ternary complex with dgtp opposite dt”. X-ray diffraction, 2 ligands (DGT, CA), 13 pockets (best druggability 0.82). MolNFT v1 #76252 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3QEX
- Type
- protein + DNA
- Length
- 932 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'- D(*TP*CP*AP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DGT, CA
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 901 | 45% helix, 19% strand | Q38087 |
| T | DNA (5'- D(*TP*CP*AP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
| P | DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') | dna | 13 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 5 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.82 | 0.93 | 38 | empty |
| 2 | 326 | 0.76 | 0.87 | 56 | DGT, CA |
| 3 | 210 | 0.70 | 0.86 | 29 | CA |
| 4 | 184 | 0.66 | 0.86 | 30 | empty |
| 5 | 442 | 0.65 | 0.78 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1345 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–P · 660 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 614 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3QEX · RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite dT · 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 3QEX · PDBe 3QEX · UniProt Q38087
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