MolNFT v1 · #65691 · protein + DNA
Ternary complex of human DNA polymerase iota with template U/T and incoming dgtp
3H4D: “Ternary complex of human DNA polymerase iota with template U/T and incoming dgtp”. X-ray diffraction, 2 ligands (DGT, MG), 6 pockets (best druggability 0.77). MolNFT v1 #65691 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3H4D
- Type
- protein + DNA
- Length
- 389 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase iota; 5'-D(*AP*GP*GP*AP*CP*CP*(DOC)); 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T)
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- DGT, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 373 | 45% helix, 19% strand | Q9UNA4 |
| P | 5'-D(*AP*GP*GP*AP*CP*CP*(DOC)) | dna | 7 | — | — |
| T | 5'-D(*TP*(BRU)P*GP*GP*GP*TP*CP*CP*T) | dna | 9 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.77 | 0.79 | 82 | MG, DGT |
| 2 | 681 | 0.72 | 0.79 | 52 | empty |
| 3 | 77 | 0.43 | 0.80 | 14 | empty |
| 4 | 71 | 0.39 | 0.78 | 13 | empty |
| 5 | 101 | 0.35 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–T · 751 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–P · 445 Ų buried · 7 hydrogen bonds · protein-nucleic
- P–T · 317 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3H4D · Ternary complex of human DNA polymerase iota with template U/T and incoming dGTP · 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 3H4D · PDBe 3H4D · UniProt Q9UNA4
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