Research workbench
Structure of the CUL1-RBX1-SKP1-F BOXSKP2 scf ubiquitin ligase complex
Analyse Structure of the CUL1-RBX1-SKP1-F BOXSKP2 scf 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
- 1LDJ
- Type
- protein
- Length
- 813 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin homolog 1; Ring-box protein 1
- UniProt
- Q13616, P62877
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cullin homolog 1 | protein | 725 | 61% helix, 6% strand | Q13616 |
| B | Ring-box protein 1 | protein | 88 | 13% helix, 23% strand | P62877 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B
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 | 760 | 0.74 | 0.79 | 61 | empty |
| 2 | 758 | 0.73 | 0.78 | 82 | empty |
| 3 | 60 | 0.52 | 0.87 | 18 | empty |
| 4 | 155 | 0.47 | 0.77 | 28 | empty |
| 5 | 59 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2495 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 1LDJ · Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P62877 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RBX1 (P62877) · a predicted model of the same protein · chain B 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 Q13616
- Every structure of UniProt P62877
- Elsewhere: RCSB PDB 1LDJ · PDBe 1LDJ · UniProt Q13616 · UniProt P62877
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