MolNFT v1 · #72700 · protein + DNA
Structural basis for proficient incorporation of dttp opposite O6- methylguanine by human DNA polymerase iota
3NGD · 5'-D(*TP*CP*TP*(6OG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*C…: “Structural basis for proficient incorporation of dttp opposite O6- methylguanine by human DNA polymerase iota”. X-ray diffraction, 1 ligand (DCP), 6 pockets (best…
- PDB
- 3NGD
- Type
- protein + DNA
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*CP*TP*(6OG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3'; DNA polymerase…
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- DCP
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*TP*CP*TP*(6OG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3' | dna | 7 | — | — |
| D | 5'-D(*TP*CP*TP*(6OG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3' | dna | 8 | — | — |
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 370 | 45% helix, 20% strand | Q9UNA4 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains C, D, A
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 | 778 | 0.74 | 0.79 | 56 | empty |
| 2 | 537 | 0.71 | 0.81 | 36 | empty |
| 3 | 440 | 0.66 | 0.79 | 37 | DCP |
| 4 | 65 | 0.46 | 0.83 | 13 | empty |
| 5 | 59 | 0.30 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- D–A · 711 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–A · 539 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 342 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3NGD · Structural Basis for Proficient Incorporation of dTTP Opposite O6-methylguanine by Human… · the same entry in another collection · chain C against C, 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 1.00
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 3NGD · PDBe 3NGD · UniProt Q9UNA4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.