Research workbench
The X-ray structure of the DDB1-DCAF1-vpr-UNG2 complex
Analyse The X-ray structure of the DDB1-DCAF1-vpr-UNG2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JK7
- Type
- protein
- Length
- 3,518 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Protein vprbp; Uracil-DNA glycosylase; Protein vpr
- EC
- 2.7.11.1, 3.2.2.27
- UniProt
- Q16531, Q9Y4B6, P13051, P12520
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA damage-binding protein 1 | protein | 1133 | 5% helix, 53% strand | Q16531 |
| C, E | Protein vprbp (EC 2.7.11.1) | protein | 331 | 5% helix, 43% strand | Q9Y4B6 |
| D, G | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 221 | 34% helix, 12% strand | P13051 |
| F, H | Protein vpr | protein | 74 | 53% helix, 0% strand | P12520 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.86 | 0.87 | 112 | empty |
| 2 | 1178 | 0.84 | 0.84 | 106 | empty |
| 3 | 904 | 0.83 | 0.85 | 64 | empty |
| 4 | 1137 | 0.83 | 0.84 | 106 | empty |
| 5 | 1126 | 0.83 | 0.84 | 100 | empty |
Interfaces
17 interfaces between chains.
- A–C · 2436 Ų buried · 31 hydrogen bonds · protein-protein
- B–E · 2416 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1720 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 1716 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1058 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5JK7 · The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y4B6 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 1 (Q9Y4B6) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q16531
- Every structure of UniProt Q9Y4B6
- Every structure of UniProt P13051
- Every structure of UniProt P12520
- Elsewhere: RCSB PDB 5JK7 · PDBe 5JK7 · UniProt Q16531 · UniProt Q9Y4B6 · UniProt P13051 · UniProt P12520
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