MolNFT v1 · #75626 · protein + DNA
Binary complex of aflatoxin B1 adduct modified DNA (AFB1-fapy) with DNA polymerase IV
3PVX: “Binary complex of aflatoxin B1 adduct modified DNA (AFB1-fapy) with DNA polymerase IV”. X-ray diffraction, 2 ligands (PVX, CA), 3 pockets (best druggability 0.76). MolNFT v1 #75626 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3PVX
- Type
- protein + DNA
- Length
- 367 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*AP*TP*TP*(PVX) P*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- PVX, CA
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 43% helix, 22% strand | Q97W02 |
| B | DNA (5'-D(*AP*TP*TP*(PVX) P*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- PVX · N-(2-amino-5-{formyl[(6as,8r,9r,9ar)-9-hydroxy-4-methoxy-1,11-dioxo-1,6A,8,9,9A,11-hexahydrocyclopenta[c]furo[3',2':4,5]furo[2,3-h]chromen-8-yl]amino}-6-oxo-1,6-dihydropyrimidin-4-yl)-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine · ligand · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.76 | 0.82 | 54 | CA |
| 2 | 284 | 0.64 | 0.81 | 32 | empty |
| 3 | 73 | 0.32 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 550 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 532 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 515 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3PVX · Binary complex of Aflatoxin B1 Adduct modified DNA (AFB1-FAPY) with DNA Polymerase IV · the same entry in another collection · chain A against A, 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 0.98
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 3PVX · PDBe 3PVX · UniProt Q97W02
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