MolNFT v1 · #65374 · protein + DNA
Human DNA polymerase iota in complex with T template DNA and incoming dttp
3GV7: “Human DNA polymerase iota in complex with T template DNA and incoming dttp”. X-ray diffraction, 2 ligands (TTP, MG), 4 pockets (best druggability 0.73). MolNFT v1 #65374 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GV7
- Type
- protein + DNA
- Length
- 393 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase iota; 5'-D(P*AP*TP*GP*GP*GP*TP*CP*CP*T)-3'; 5'-D(*AP*GP*GP*AP*CP*CP*C)-3'
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- TTP, MG
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase iota (EC 2.7.7.7) | protein | 377 | 44% helix, 21% strand | Q9UNA4 |
| T | 5'-D(P*AP*TP*GP*GP*GP*TP*CP*CP*T)-3' | dna | 9 | — | — |
| P | 5'-D(*AP*GP*GP*AP*CP*CP*C)-3' | dna | 7 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains B, T, P
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.73 | 0.79 | 58 | empty |
| 2 | 577 | 0.71 | 0.80 | 37 | empty |
| 3 | 418 | 0.69 | 0.81 | 34 | TTP, MG |
| 4 | 74 | 0.29 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–T · 817 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–P · 515 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–P · 327 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Compared structures
- 3GV7 · Human DNA polymerase iota in complex with T template DNA and incoming dTTP · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · a predicted model of the same protein · chain B 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 Q9UNA4
- Elsewhere: RCSB PDB 3GV7 · PDBe 3GV7 · UniProt Q9UNA4
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