Research workbench
Structural insights into NEDD8 activation of cullin-ring ligases: conformational control of conjugation.
Analyse Structural insights into NEDD8 activation of cullin-ring ligases… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DPL
- Type
- protein
- Length
- 465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-5; Ring-box protein 1
- UniProt
- Q93034, P62877
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cullin-5 | protein | 378 | 52% helix, 16% strand | Q93034 |
| R | Ring-box protein 1 | protein | 87 | 14% helix, 30% strand | P62877 |
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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.75 | 0.81 | 62 | empty |
| 2 | 280 | 0.69 | 0.84 | 25 | empty |
| 3 | 325 | 0.56 | 0.75 | 32 | ZN |
| 4 | 159 | 0.48 | 0.77 | 29 | empty |
| 5 | 79 | 0.39 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- C–R · 2412 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3DPL · Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control… · 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 0.93
- 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 0.76
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 P62877
- Elsewhere: RCSB PDB 3DPL · PDBe 3DPL · UniProt Q93034 · UniProt P62877
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.