Research workbench
FBXW11-SKP1 in complex with a PSER33/PSER37 beta-catenin peptide
Analyse FBXW11-SKP1 in complex with a PSER33/PSER37 beta-catenin peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WNX
- Type
- protein
- Length
- 1,659 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F-BOX/WD repeat-containing protein 11; S-phase kinase-associated protein 1; Catenin beta-1
- UniProt
- Q9UKB1, P63208, P35222
- Ligands
- NA
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F-BOX/WD repeat-containing protein 11 | protein | 410 | 21% helix, 41% strand | Q9UKB1 |
| B | S-phase kinase-associated protein 1 | protein | 142 | 58% helix, 8% strand | P63208 |
| C, F, I | Catenin beta-1 | protein | 9 | 0% helix, 0% strand | P35222 |
| D | F-BOX/WD repeat-containing protein 11 | protein | 402 | 21% helix, 41% strand | Q9UKB1 |
| E | S-phase kinase-associated protein 1 | protein | 130 | 55% helix, 8% strand | P63208 |
| G | F-BOX/WD repeat-containing protein 11 | protein | 404 | 22% helix, 41% strand | Q9UKB1 |
| H | S-phase kinase-associated protein 1 | protein | 144 | 59% helix, 10% strand | P63208 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, D
- GOL · Glycerol · additive · 6 copies · chains A, B, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.74 | 0.79 | 85 | empty |
| 2 | 947 | 0.72 | 0.76 | 83 | empty |
| 3 | 383 | 0.64 | 0.79 | 59 | GOL |
| 4 | 414 | 0.64 | 0.78 | 62 | empty |
| 5 | 315 | 0.62 | 0.79 | 47 | empty |
Interfaces
10 interfaces between chains.
- G–H · 1702 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1659 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1406 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 682 Ų buried · 18 hydrogen bonds · protein-protein
- G–I · 654 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 6WNX · FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide · the same entry in another collection · chain I against I, TM-score 1.00
- Q9UKB1 · AlphaFold monomer V2.0 prediction for F-BOX/WD repeat-containing protein 11 (Q9UKB1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UKB1
- Every structure of UniProt P63208
- Every structure of UniProt P35222
- Elsewhere: RCSB PDB 6WNX · PDBe 6WNX · UniProt Q9UKB1 · UniProt P63208 · UniProt P35222
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