Research workbench
Crystal structure of DPO4 extension past 8-oxoadenine (oxoa) and dg
Analyse Crystal structure of DPO4 extension past 8-oxoadenine (oxoa) and dg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VKP
- Type
- protein + DNA
- Length
- 746 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*AP*GP*AP*TP*TP*CP*G)-3'); DNA (5'-D(*TP*TP*CP*AP*TP*(A38)…
- EC
- 2.7.7.7
- UniProt
- A0A0E3K6E9
- Ligands
- DZ4, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, B | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*AP*GP*AP*TP*TP*CP*G)-3') | dna | 14 | — | — |
| T, C | DNA (5'-D(*TP*TP*CP*AP*TP*(A38) P*GP*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 18 | — | — |
| A, D | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 44% helix, 23% strand | A0A0E3K6E9 |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 2 copies · chains P, T, A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains P, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.80 | 0.82 | 72 | MG, DZ4 |
| 2 | 1093 | 0.79 | 0.81 | 76 | MG, DZ4 |
| 3 | 608 | 0.75 | 0.82 | 43 | empty |
| 4 | 617 | 0.75 | 0.82 | 44 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1098 Ų buried · 26 hydrogen bonds · protein-nucleic
- T–A · 1052 Ų buried · 26 hydrogen bonds · protein-nucleic
- P–A · 667 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 657 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 571 Ų buried · 58 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6VKP · Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dG · the same entry in another collection · chain D against D, 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 6VKP · PDBe 6VKP · UniProt A0A0E3K6E9
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