MolNFT v1 · #52724 · protein + DNA
Binary complex of DPO4 bound to N2,N2-dimethyl- deoxyguanosine modified DNA
2W9B · DNA polymerase IV: “Binary complex of DPO4 bound to N2,N2-dimethyl- deoxyguanosine modified DNA”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.81). MolNFT v1 #52724 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2W9B
- Type
- protein + DNA
- Length
- 743 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*CP*DOCP)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- MG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 38% helix, 22% strand | Q97W02 |
| B | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 35% helix, 18% strand | Q97W02 |
| C, D | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOCP)-3' | dna | 14 | — | — |
| E, F | 5'-D(*TP*CP*AP*TP*M2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | dna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.81 | 0.82 | 71 | MG |
| 2 | 915 | 0.79 | 0.82 | 73 | MG |
| 3 | 452 | 0.75 | 0.85 | 40 | empty |
| 4 | 370 | 0.69 | 0.82 | 36 | empty |
| 5 | 75 | 0.42 | 0.80 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–F · 1015 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–E · 941 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 721 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 715 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–E · 596 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2W9B · Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA · 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 A 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 2W9B · PDBe 2W9B · UniProt Q97W02
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