MolNFT v1 · #167287 · protein + DNA
Crystal structure of DPO4 with 8-oxoadenine (oxoa) and dgtp*
6VG6 · DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'): “Crystal structure of DPO4 with 8-oxoadenine (oxoa) and dgtp*”. X-ray diffraction, 2 ligands (XG4, MG), 7 pockets (best druggability 0.82). MolNFT v1 #167287 on GenesisL1: 3D…
- PDB
- 6VG6
- Type
- protein + DNA
- Length
- 740 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'); DNA (5'-D(*TP*CP*AP*TP*(A38)…
- EC
- 2.7.7.7
- UniProt
- A0A0E3K6E9
- Ligands
- XG4, MG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, B | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') | dna | 13 | — | — |
| T, C | DNA (5'-D(*TP*CP*AP*TP*(A38) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 16 | — | — |
| A, D | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 43% helix, 23% strand | A0A0E3K6E9 |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · 2 copies · chains P, T, A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains P, A, B, D
- GOL · Glycerol · additive · 2 copies · chains P, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.82 | 0.83 | 63 | XG4, GOL |
| 2 | 1041 | 0.81 | 0.82 | 69 | XG4, MG |
| 3 | 603 | 0.72 | 0.80 | 37 | empty |
| 4 | 543 | 0.71 | 0.80 | 35 | empty |
| 5 | 99 | 0.47 | 0.81 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1033 Ų buried · 20 hydrogen bonds · protein-nucleic
- T–A · 1025 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–D · 631 Ų buried · 20 hydrogen bonds · protein-nucleic
- P–A · 616 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 575 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6VG6 · Crystal structure of DPO4 with 8-oxoadenine (oxoA) and dGTP* · 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 6VG6 · PDBe 6VG6 · UniProt A0A0E3K6E9
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