Research workbench
Crystal structure of DPO4 with 8-oxoadenine (oxoa) and dttp*
Analyse Crystal structure of DPO4 with 8-oxoadenine (oxoa) and dttp* in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VGM
- Type
- protein + DNA
- Length
- 740 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- A0A0E3K6E9
- Ligands
- 1FZ, MG
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 43% helix, 23% strand | A0A0E3K6E9 |
| B, P | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') | dna | 13 | — | — |
| C, T | 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 | — | — |
Ligands and binding sites
- 1FZ · 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine · ligand · 2 copies · chains A, P, T, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, P, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 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 | 0.83 | 0.84 | 70 | 1FZ, MG |
| 2 | 1044 | 0.82 | 0.84 | 67 | 1FZ, MG |
| 3 | 696 | 0.74 | 0.80 | 40 | empty |
| 4 | 672 | 0.74 | 0.80 | 43 | empty |
| 5 | 50 | 0.25 | 0.73 | 14 | empty |
Interfaces
7 interfaces between chains.
- A–T · 1031 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–D · 1013 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–D · 627 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 590 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 574 Ų buried · 62 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6VGM · Crystal structure of DPO4 with 8-oxoadenine (oxoA) and dTTP* · the same entry in another collection · chain A against A, 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 6VGM · PDBe 6VGM · UniProt A0A0E3K6E9
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