MolNFT v1 · #65372 · protein + DNA
Human DNA polymerase iota in complex with T template DNA and incoming ddadp
3GV5: “Human DNA polymerase iota in complex with T template DNA and incoming ddadp”. X-ray diffraction, 2 ligands (ADI, CA), 10 pockets (best druggability 0.80). MolNFT v1 #65372 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3GV5
- Type
- protein + DNA
- Length
- 806 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase iota; 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- ADI, CA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase iota (EC 2.7.7.7) | protein | 379 | 44% helix, 21% strand | Q9UNA4 |
| P, E | 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3' | dna | 9 | — | — |
| T, F | 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3' | dna | 13 | — | — |
| D | DNA polymerase iota (EC 2.7.7.7) | protein | 383 | 44% helix, 21% strand | Q9UNA4 |
Ligands and binding sites
- ADI · 2',3'-dideoxyadenosine-5'-diphosphate · ligand · 2 copies · chains B, P, T, D, E, F
- CA · Calcium ion · metal · 8 copies · chains B, P, D, E, F
- GOL · Glycerol · additive · chains B, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.80 | 0.82 | 88 | CA, ADI |
| 2 | 389 | 0.76 | 0.86 | 40 | CA |
| 3 | 755 | 0.74 | 0.80 | 54 | empty |
| 4 | 362 | 0.72 | 0.84 | 44 | CA |
| 5 | 186 | 0.67 | 0.86 | 25 | CA, ADI |
Interfaces
7 interfaces between chains.
- B–T · 922 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–F · 916 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–P · 640 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–E · 626 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 422 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3GV5 · Human DNA polymerase iota in complex with T template DNA and incoming ddADP · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 3GV5 · PDBe 3GV5 · UniProt Q9UNA4
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