MolNFT v1 · #94768 · protein
A ubiquitin ligase-substrate complex
4I6J · Cryptochrome-2: “A ubiquitin ligase-substrate complex”. X-ray diffraction, 10 pockets (best druggability 0.78). MolNFT v1 #94768 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4I6J
- Type
- protein
- Length
- 1,027 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptochrome-2; F-BOX/LRR-repeat protein 3; S-phase kinase-associated protein 1
- UniProt
- Q9R194, Q9UKT7, P63208
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cryptochrome-2 | protein | 503 | 47% helix, 6% strand | Q9R194 |
| B | F-BOX/LRR-repeat protein 3 | protein | 394 | 39% helix, 17% strand | Q9UKT7 |
| C | S-phase kinase-associated protein 1 | protein | 130 | 38% helix, 3% strand | P63208 |
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.78 | 0.80 | 78 | empty |
| 2 | 667 | 0.75 | 0.81 | 45 | empty |
| 3 | 346 | 0.74 | 0.85 | 52 | empty |
| 4 | 551 | 0.70 | 0.79 | 55 | empty |
| 5 | 286 | 0.63 | 0.80 | 38 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2647 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1665 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4I6J · A ubiquitin ligase-substrate complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKT7 · AlphaFold monomer V2.0 prediction for F-BOX/LRR-repeat protein 3 (Q9UKT7) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q9R194 · AlphaFold monomer V2.0 prediction for cryptochrome-2 (Q9R194) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 Q9R194
- Every structure of UniProt Q9UKT7
- Every structure of UniProt P63208
- Elsewhere: RCSB PDB 4I6J · PDBe 4I6J · UniProt Q9R194 · UniProt Q9UKT7 · UniProt P63208
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