Research workbench
Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi- cullin-ring E3-catalyzed ubiquitin ligation
Analyse Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z8B
- Type
- protein
- Length
- 1,896 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-7; F-BOX/WD repeat-containing protein 8; E3 ubiquitin-protein ligase RBX1; S-phase…
- EC
- 2.3.2.27, 2.3.2.32
- UniProt
- Q14999, Q8N3Y1, P62877, P63208
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cullin-7 | protein | 1224 | 54% helix, 11% strand | Q14999 |
| F | F-BOX/WD repeat-containing protein 8 | protein | 457 | 15% helix, 39% strand | Q8N3Y1 |
| R | E3 ubiquitin-protein ligase RBX1 (EC 2.3.2.27, 2.3.2.32) | protein | 86 | 17% helix, 22% strand | P62877 |
| S | S-phase kinase-associated protein 1 | protein | 129 | 57% helix, 8% strand | P63208 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.80 | 0.83 | 94 | empty |
| 2 | 130 | 0.78 | 0.95 | 31 | empty |
| 3 | 739 | 0.76 | 0.81 | 71 | empty |
| 4 | 1154 | 0.75 | 0.78 | 105 | empty |
| 5 | 817 | 0.74 | 0.79 | 48 | empty |
Interfaces
3 interfaces between chains.
- C–F · 3598 Ų buried · 29 hydrogen bonds · protein-protein
- C–R · 2142 Ų buried · 33 hydrogen bonds · protein-protein
- F–S · 1123 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7Z8B · Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8N3Y1 · AlphaFold monomer V2.0 prediction for F-BOX/WD repeat-containing protein 8 (Q8N3Y1) · a predicted model of the same protein · chain F against A, TM-score 0.89
- Q14999 · AlphaFold monomer V2.0 prediction for cullin-7 (Q14999) · a predicted model of the same protein · chain C against A, TM-score 0.84
- P62877 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RBX1 (P62877) · a predicted model of the same protein · chain R 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 Q14999
- Every structure of UniProt Q8N3Y1
- Every structure of UniProt P62877
- Every structure of UniProt P63208
- Elsewhere: RCSB PDB 7Z8B · PDBe 7Z8B · UniProt Q14999 · UniProt Q8N3Y1 · UniProt P62877 · UniProt P63208
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