Research workbench
Human DNA polymerase iota incorporating dctp opposite N- (deoxyguanosin-8-yl)-1-aminopyrene lesion
Analyse Human DNA polymerase iota incorporating dctp opposite N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EYH
- Type
- protein + DNA
- Length
- 392 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase iota; DNA template; DNA primer
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- DCP, MG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase iota (EC 2.7.7.7) | protein | 377 | 42% helix, 19% strand | Q9UNA4 |
| T | DNA template | dna | 8 | — | — |
| P | DNA primer | dna | 7 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains B, T, P
- MG · Magnesium ion · metal · 3 copies · chains B, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.81 | 0.83 | 76 | DCP, MG |
| 2 | 507 | 0.73 | 0.82 | 36 | empty |
| 3 | 128 | 0.70 | 0.90 | 23 | empty |
| 4 | 56 | 0.47 | 0.84 | 15 | empty |
| 5 | 66 | 0.32 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–T · 699 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–P · 524 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 327 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 4EYH · PDBe 4EYH · UniProt Q9UNA4
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