MolNFT v1 · #167528 · protein + DNA
Crystal structure of DPO4 extension past 8-oxoadenine (oxoa) and dt
6VNP · DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3'): “Crystal structure of DPO4 extension past 8-oxoadenine (oxoa) and dt”. X-ray diffraction, 2 ligands (DZ4, MG), 12 pockets (best druggability 0.81). MolNFT v1 #167528 on…
- PDB
- 6VNP
- Type
- protein + DNA
- Length
- 1,489 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3'); DNA (5'-D(*TP*TP*CP*AP*T*(R5M)…
- EC
- 2.7.7.7
- UniProt
- A0A0E3K6E9
- Ligands
- DZ4, MG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, B, E, H | DNA (5'-D(P*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*T)-3') | dna | 14 | — | — |
| T, F, I | DNA (5'-D(*TP*TP*CP*AP*T*(R5M) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 17 | — | — |
| A, D, G, J | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 46% helix, 25% strand | A0A0E3K6E9 |
| C | DNA (5'-D(*TP*TP*CP*AP*T*(R5M) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 4 copies · chains P, T, A, B, C, D, E, F, G, H, I, J
- MG · Magnesium ion · metal · 8 copies · chains P, A, D, B, G, E, J, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.81 | 0.82 | 73 | DZ4, MG |
| 2 | 1120 | 0.80 | 0.82 | 79 | DZ4, MG |
| 3 | 1138 | 0.80 | 0.82 | 82 | DZ4, MG |
| 4 | 1172 | 0.80 | 0.82 | 67 | DZ4, MG |
| 5 | 600 | 0.76 | 0.83 | 38 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1051 Ų buried · 25 hydrogen bonds · protein-nucleic
- T–A · 983 Ų buried · 24 hydrogen bonds · protein-nucleic
- I–J · 976 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–G · 961 Ų buried · 22 hydrogen bonds · protein-nucleic
- H–J · 644 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6VNP · Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT · the same entry in another collection · chain P against P, 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 A0A0E3K6E9
- Elsewhere: RCSB PDB 6VNP · PDBe 6VNP · UniProt A0A0E3K6E9
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