Research workbench
Cryoem structure of DDB1-vprbp-vpr-UNG2(94-313) complex
Analyse Cryoem structure of DDB1-vprbp-vpr-UNG2(94-313) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V7C
- Type
- protein
- Length
- 5,084 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DDB1- and CUL4-associated factor 1; DNA damage-binding protein 1; Protein vpr; Uracil-DNA…
- EC
- 2.7.11.1, 3.2.2.27
- UniProt
- Q9Y4B6, Q16531, B2CPZ1, P13051
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 24% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DDB1- and CUL4-associated factor 1 (EC 2.7.11.1) | protein | 1110 | 42% helix, 13% strand | Q9Y4B6 |
| B, F | DNA damage-binding protein 1 | protein | 1133 | 4% helix, 41% strand | Q16531 |
| C, G | Protein vpr | protein | 79 | 53% helix, 1% strand | B2CPZ1 |
| D, H | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 220 | 28% helix, 5% strand | P13051 |
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 | 908 | 0.85 | 0.87 | 79 | empty |
| 2 | 1109 | 0.85 | 0.86 | 79 | empty |
| 3 | 799 | 0.84 | 0.87 | 96 | empty |
| 4 | 997 | 0.82 | 0.83 | 87 | empty |
| 5 | 1165 | 0.82 | 0.83 | 116 | empty |
Interfaces
14 interfaces between chains.
- A–E · 3967 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3625 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 3622 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1754 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 1751 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7V7C · CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex · the same entry in another collection · chain H against H, TM-score 1.00
- P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · a predicted model of the same protein · chain D against A, TM-score 0.93
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain F against A, TM-score 0.93
- Q9Y4B6 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 1 (Q9Y4B6) · a predicted model of the same protein · chain E against A, TM-score 0.62
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 Q9Y4B6
- Every structure of UniProt Q16531
- Every structure of UniProt B2CPZ1
- Every structure of UniProt P13051
- Elsewhere: RCSB PDB 7V7C · PDBe 7V7C · UniProt Q9Y4B6 · UniProt Q16531 · UniProt B2CPZ1 · UniProt P13051
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