MolNFT v1 · #90932 · protein + DNA
Human DNA polymerase iota incorporating datp opposite N- (deoxyguanosin-8-yl)-1-aminopyrene lesion
4EYI: “Human DNA polymerase iota incorporating datp opposite N- (deoxyguanosin-8-yl)-1-aminopyrene lesion”. X-ray diffraction, 2 ligands (DTP, MG), 7 pockets (best druggability 0.79). MolNFT v1 #90932 on GenesisL1: 3D structure, binding…
- PDB
- 4EYI
- Type
- protein + DNA
- Length
- 393 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
- DTP, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase iota (EC 2.7.7.7) | protein | 378 | 42% helix, 20% strand | Q9UNA4 |
| T | DNA template | dna | 8 | — | — |
| P | DNA primer | dna | 7 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.79 | 0.81 | 84 | DTP, MG |
| 2 | 501 | 0.69 | 0.80 | 35 | empty |
| 3 | 81 | 0.56 | 0.86 | 13 | empty |
| 4 | 52 | 0.35 | 0.79 | 20 | empty |
| 5 | 72 | 0.33 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–T · 618 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–P · 512 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 367 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 4EYI · PDBe 4EYI · UniProt Q9UNA4
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