Research workbench
Structure of human DNA polymerase iota complexed with N2-ethylguanine
Analyse Structure of human DNA polymerase iota complexed with N2-ethylguanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EPG
- Type
- protein + DNA
- Length
- 390 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase iota; 5'-D(*DTP*DCP*DTP*(2EG) P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP…
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- DCP, NA
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 375 | 46% helix, 19% strand | Q9UNA4 |
| B | 5'-D(*DTP*DCP*DTP*(2EG) P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3' | dna | 7 | — | — |
| C | 5'-D(*DTP*DCP*DTP*(2EG) P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3' | dna | 8 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.78 | 0.80 | 74 | DCP, NA |
| 2 | 734 | 0.73 | 0.79 | 56 | NA |
| 3 | 66 | 0.33 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 723 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 507 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 326 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3EPG · Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · a predicted model of the same protein · chain A 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 3EPG · PDBe 3EPG · UniProt Q9UNA4
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