MolNFT v1 · #184352 · protein
Structure of neddylated CUL5 C-terminal region-RBX2-ARIH2*
7ONI · Cullin-5: “Structure of neddylated CUL5 C-terminal region-RBX2-ARIH2*”. Electron microscopy, 1 ligand (ZN), 16 pockets (best druggability 0.76). MolNFT v1 #184352 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ONI
- Type
- protein
- Length
- 1,141 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-5; E3 ubiquitin-protein ligase ARIH2; Ring-box protein 2; NEDD8
- EC
- 2.3.2.31
- UniProt
- Q93034, O95376, Q9UBF6, Q15843
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cullin-5 | protein | 599 | 61% helix, 7% strand | Q93034 |
| H | E3 ubiquitin-protein ligase ARIH2 (EC 2.3.2.31) | protein | 380 | 55% helix, 6% strand | O95376 |
| R | Ring-box protein 2 | protein | 86 | 19% helix, 24% strand | Q9UBF6 |
| N | NEDD8 | protein | 76 | 24% helix, 33% strand | Q15843 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains H, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.76 | 0.78 | 100 | empty |
| 2 | 65 | 0.67 | 0.94 | 15 | empty |
| 3 | 439 | 0.62 | 0.76 | 58 | empty |
| 4 | 55 | 0.62 | 0.93 | 17 | empty |
| 5 | 324 | 0.61 | 0.78 | 39 | empty |
Interfaces
4 interfaces between chains.
- C–R · 2152 Ų buried · 30 hydrogen bonds · protein-protein
- C–H · 1375 Ų buried · 12 hydrogen bonds · protein-protein
- C–N · 852 Ų buried · 7 hydrogen bonds · protein-protein
- H–R · 712 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 7ONI · Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2* · the same entry in another collection · chain N against N, TM-score 1.00
- Q15843 · AlphaFold monomer V2.0 prediction for NEDD8 (Q15843) · a predicted model of the same protein · chain N against A, TM-score 0.93
- O95376 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ARIH2 (O95376) · a predicted model of the same protein · chain H against A, TM-score 0.91
- Q93034 · AlphaFold monomer V2.0 prediction for cullin-5 (Q93034) · a predicted model of the same protein · chain C against A, TM-score 0.84
- Q9UBF6 · AlphaFold monomer V2.0 prediction for ring-box protein 2 (Q9UBF6) · a predicted model of the same protein · chain R against A, TM-score 0.76
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 Q93034
- Every structure of UniProt O95376
- Every structure of UniProt Q9UBF6
- Every structure of UniProt Q15843
- Elsewhere: RCSB PDB 7ONI · PDBe 7ONI · UniProt Q93034 · UniProt O95376 · UniProt Q9UBF6 · UniProt Q15843
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