Research workbench
Crystal structure of the CUL2-RBX1-elobc-vhl ubiquitin ligase complex
Analyse Crystal structure of the CUL2-RBX1-elobc-vhl ubiquitin ligase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N4W
- Type
- protein
- Length
- 967 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-2; Von hippel-lindau disease tumor suppressor; E3 ubiquitin-protein ligase RBX1…
- EC
- 6.3.2.-
- UniProt
- Q13617, P40337, P62877, Q15370, Q15369
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cullin-2 | protein | 671 | 58% helix, 3% strand | Q13617 |
| V | Von hippel-lindau disease tumor suppressor | protein | 37 | 24% helix, 0% strand | P40337 |
| R | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 86 | 19% helix, 16% strand | P62877 |
| B | Elongin-B | protein | 82 | 18% helix, 15% strand | Q15370 |
| C | Elongin-C | protein | 91 | 41% helix, 8% strand | Q15369 |
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
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.77 | 0.79 | 90 | empty |
| 2 | 1037 | 0.77 | 0.79 | 80 | empty |
| 3 | 99 | 0.76 | 0.96 | 18 | empty |
| 4 | 87 | 0.72 | 0.95 | 18 | empty |
| 5 | 201 | 0.61 | 0.82 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–R · 2235 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1099 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 964 Ų buried · 7 hydrogen bonds · protein-protein
- V–C · 655 Ų buried · 7 hydrogen bonds · protein-protein
- A–V · 363 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5N4W · Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex · the same entry in another collection · chain R against R, TM-score 1.00
- Q13617 · AlphaFold monomer V2.0 prediction for cullin-2 (Q13617) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain C against A, TM-score 0.90
- Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain B against A, TM-score 0.87
- 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 0.68
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 Q13617
- Every structure of UniProt P40337
- Every structure of UniProt P62877
- Every structure of UniProt Q15370
- Every structure of UniProt Q15369
- Elsewhere: RCSB PDB 5N4W · PDBe 5N4W · UniProt Q13617 · UniProt P40337 · UniProt P62877 · UniProt Q15370 · UniProt Q15369
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