Research workbench
Structure of the CAND1-CUL4B-RBX1 complex
Analyse Structure of the CAND1-CUL4B-RBX1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A0C
- Type
- protein
- Length
- 3,866 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-associated NEDD8-dissociated protein 1; Cullin-4B; E3 ubiquitin-protein ligase RBX1
- EC
- 6.3.2.-
- UniProt
- Q86VP6, Q13620, P62878
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cullin-associated NEDD8-dissociated protein 1 | protein | 1155 | 68% helix, 1% strand | Q86VP6 |
| B | Cullin-associated NEDD8-dissociated protein 1 | protein | 1154 | 67% helix, 0% strand | Q86VP6 |
| C | Cullin-4B | protein | 692 | 57% helix, 7% strand | Q13620 |
| D | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 89 | 17% helix, 21% strand | P62878 |
| E | Cullin-4B | protein | 696 | 59% helix, 7% strand | Q13620 |
| F | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 80 | 16% helix, 26% strand | P62878 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.85 | 0.86 | 93 | empty |
| 2 | 956 | 0.82 | 0.83 | 89 | empty |
| 3 | 1069 | 0.82 | 0.83 | 104 | empty |
| 4 | 886 | 0.81 | 0.83 | 92 | empty |
| 5 | 913 | 0.80 | 0.82 | 119 | empty |
Interfaces
9 interfaces between chains.
- A–E · 3783 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 3614 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2846 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2662 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 344 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4A0C · Structure of the CAND1-CUL4B-RBX1 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q13620 · AlphaFold monomer V2.0 prediction for cullin-4B (Q13620) · a predicted model of the same protein · chain E against A, TM-score 0.96
- Q86VP6 · AlphaFold monomer V2.0 prediction for cullin-associated NEDD8-dissociated protein 1… · a predicted model of the same protein · chain B against A, TM-score 0.81
- P62878 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RBX1 (P62878) · a predicted model of the same protein · chain D against A, TM-score 0.73
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 Q86VP6
- Every structure of UniProt Q13620
- Every structure of UniProt P62878
- Elsewhere: RCSB PDB 4A0C · PDBe 4A0C · UniProt Q86VP6 · UniProt Q13620 · UniProt P62878
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