MolNFT v1 · #156589 · protein
Monophosphorylated PSER33 B-catenin peptide, B-TRCP/SKP1, nrx-2663 ternary complex
6M92 · F-BOX/WD repeat-containing protein 1A: “Monophosphorylated PSER33 B-catenin peptide, B-TRCP/SKP1, nrx-2663 ternary complex”. X-ray diffraction, 2 ligands (J8V, PO4), 3 pockets (best druggability 0.53). MolNFT v1 #156589 on…
- PDB
- 6M92
- Type
- protein
- Length
- 544 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F-BOX/WD repeat-containing protein 1A; S-phase kinase-associated protein 1; Catenin beta-1
- UniProt
- Q9Y297, P63208, P35222
- Ligands
- J8V, PO4
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F-BOX/WD repeat-containing protein 1A | protein | 401 | 23% helix, 42% strand | Q9Y297 |
| B | S-phase kinase-associated protein 1 | protein | 133 | 58% helix, 9% strand | P63208 |
| C | Catenin beta-1 | protein | 10 | 0% helix, 0% strand | P35222 |
Ligands and binding sites
- J8V · 3-{[2-oxo-4-phenoxy-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid · ligand · chains A, C
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.53 | 0.74 | 41 | PO4 |
| 2 | 55 | 0.36 | 0.79 | 14 | empty |
| 3 | 66 | 0.31 | 0.75 | 22 | J8V |
Interfaces
2 interfaces between chains.
- A–B · 1433 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 560 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6M92 · Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y297 · AlphaFold monomer V2.0 prediction for F-BOX/WD repeat-containing protein 1A (Q9Y297) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P35222 · AlphaFold monomer V2.0 prediction for catenin beta-1 (P35222) · a predicted model of the same protein · chain C against A, TM-score 0.38
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 Q9Y297
- Every structure of UniProt P63208
- Every structure of UniProt P35222
- Elsewhere: RCSB PDB 6M92 · PDBe 6M92 · UniProt Q9Y297 · UniProt P63208 · UniProt P35222
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