Research workbench
Cryoem structure of DDB1-vprbp complex in arm-up conformation
Analyse Cryoem structure of DDB1-vprbp complex in arm-up conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V7B
- Type
- protein
- Length
- 4,486 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DDB1- and CUL4-associated factor 1; DNA damage-binding protein 1
- EC
- 2.7.11.1
- UniProt
- Q9Y4B6, Q16531
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 21% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DDB1- and CUL4-associated factor 1 (EC 2.7.11.1) | protein | 1110 | 39% helix, 12% strand | Q9Y4B6 |
| B, D | DNA damage-binding protein 1 | protein | 1133 | 4% helix, 37% strand | Q16531 |
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 | 917 | 0.85 | 0.87 | 102 | empty |
| 2 | 649 | 0.82 | 0.87 | 54 | empty |
| 3 | 620 | 0.82 | 0.87 | 52 | empty |
| 4 | 580 | 0.82 | 0.87 | 84 | empty |
| 5 | 1156 | 0.81 | 0.82 | 105 | empty |
Interfaces
5 interfaces between chains.
- A–C · 3913 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 3700 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3700 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 202 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7V7B · CryoEM structure of DDB1-VprBP complex in ARM-up conformation · the same entry in another collection · chain D against D, TM-score 1.00
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain D 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 C 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
- Elsewhere: RCSB PDB 7V7B · PDBe 7V7B · UniProt Q9Y4B6 · UniProt Q16531
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