Research workbench
Cryo-EM structure of CULLIN5 bound to ring-box protein 2 (CUL5-RBX2)
Analyse Cryo-EM structure of CULLIN5 bound to ring-box protein 2 (CUL5-RBX2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V9I
- Type
- protein
- Length
- 814 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G-binding protein G,CULLIN-5; Ring-box protein 2
- UniProt
- P06654, Q93034, Q9WTZ1
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 62% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Immunoglobulin G-binding protein G,CULLIN-5 | protein | 730 | 67% helix, 8% strand | P06654, Q93034 |
| R | Ring-box protein 2 | protein | 84 | 14% helix, 33% strand | Q9WTZ1 |
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
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.82 | 0.83 | 146 | empty |
| 2 | 1037 | 0.81 | 0.83 | 148 | empty |
| 3 | 1127 | 0.81 | 0.82 | 137 | empty |
| 4 | 992 | 0.76 | 0.79 | 132 | empty |
| 5 | 158 | 0.53 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- C–R · 1109 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6V9I · cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) · the same entry in another collection · chain C against C, TM-score 1.00
- Q93034 · AlphaFold monomer V2.0 prediction for cullin-5 (Q93034) · a predicted model of the same protein · chain C against A, TM-score 0.83
- Q9WTZ1 · AlphaFold monomer V2.0 prediction for ring-box protein 2 (Q9WTZ1) · a predicted model of the same protein · chain R against A, TM-score 0.75
- P06654 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P06654) · a predicted model of the same protein · chain C against A, TM-score 0.18
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 P06654
- Every structure of UniProt Q93034
- Every structure of UniProt Q9WTZ1
- Elsewhere: RCSB PDB 6V9I · PDBe 6V9I · UniProt P06654 · UniProt Q93034 · UniProt Q9WTZ1
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