MolNFT v1 · #52725 · protein + DNA
Ternary complex of DPO4 bound to N2,N2-dimethyl- deoxyguanosine modified DNA with incoming dttp
2W9C · DNA polymerase IV: “Ternary complex of DPO4 bound to N2,N2-dimethyl- deoxyguanosine modified DNA with incoming dttp”. X-ray diffraction, 2 ligands (TTP, MG), 4 pockets (best druggability 0.77). MolNFT v1 #52725 on GenesisL1: 3D…
- PDB
- 2W9C
- Type
- protein + DNA
- Length
- 740 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- TTP, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 39% helix, 23% strand | Q97W02 |
| B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 37% helix, 23% strand | Q97W02 |
| C, D | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3' | dna | 13 | — | — |
| E, F | 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | dna | 16 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, C, E, B, D, F
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.77 | 0.80 | 81 | MG, TTP |
| 2 | 1191 | 0.77 | 0.79 | 73 | MG, TTP |
| 3 | 424 | 0.70 | 0.81 | 37 | empty |
| 4 | 449 | 0.68 | 0.80 | 39 | empty |
Interfaces
6 interfaces between chains.
- A–E · 1002 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–F · 987 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–F · 571 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–E · 569 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–C · 549 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2W9C · Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming… · the same entry in another collection · chain F against F, TM-score 1.00
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q97W02
- Elsewhere: RCSB PDB 2W9C · PDBe 2W9C · UniProt Q97W02
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.