MolNFT v1 · #168338 · protein
Structure of a substrate-bound dqc ubiquitin ligase
6WCQ · S-phase kinase-associated protein 1: “Structure of a substrate-bound dqc ubiquitin ligase”. Electron microscopy, 8 pockets (best druggability 0.73). MolNFT v1 #168338 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WCQ
- Type
- protein
- Length
- 1,014 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-phase kinase-associated protein 1; F-BOX/LRR-repeat protein 17; Kelch-like…
- UniProt
- P63208, Q9UF56, Q14145, Q13616
- Pockets
- 8 · best druggability 0.73
Structure
electron microscopy · 4 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-phase kinase-associated protein 1 | protein | 154 | 52% helix, 6% strand | P63208 |
| B | F-BOX/LRR-repeat protein 17 | protein | 372 | 43% helix, 13% strand | Q9UF56 |
| C | Kelch-like ech-associated protein 1 | protein | 130 | 48% helix, 19% strand | Q14145 |
| D | Cullin-1 | protein | 358 | 70% helix, 0% strand | Q13616 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.73 | 0.80 | 49 | empty |
| 2 | 745 | 0.70 | 0.77 | 58 | empty |
| 3 | 293 | 0.60 | 0.79 | 28 | empty |
| 4 | 209 | 0.60 | 0.81 | 33 | empty |
| 5 | 196 | 0.56 | 0.79 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1533 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1296 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 706 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 177 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6WCQ · Structure of a substrate-bound DQC ubiquitin ligase · 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 D against A, TM-score 0.98
- Q9UF56 · AlphaFold monomer V2.0 prediction for F-BOX/LRR-repeat protein 17 (Q9UF56) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P63208
- Every structure of UniProt Q9UF56
- Every structure of UniProt Q14145
- Every structure of UniProt Q13616
- Elsewhere: RCSB PDB 6WCQ · PDBe 6WCQ · UniProt P63208 · UniProt Q9UF56 · UniProt Q14145 · UniProt Q13616
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