MolNFT v1 · #137805 · protein
Crystal structure of the SKP1-FBXO31 complex
5VZT · S-phase kinase-associated protein 1: “Crystal structure of the SKP1-FBXO31 complex”. X-ray diffraction, 2 ligands (ZN, PO4), 11 pockets (best druggability 0.84). MolNFT v1 #137805 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VZT
- Type
- protein
- Length
- 1,123 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-phase kinase-associated protein 1; F-box only protein 31
- UniProt
- P63208, Q5XUX0
- Ligands
- ZN, PO4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-phase kinase-associated protein 1 | protein | 145 | 55% helix, 8% strand | P63208 |
| B | F-box only protein 31 | protein | 418 | 30% helix, 30% strand | Q5XUX0 |
| C | S-phase kinase-associated protein 1 | protein | 143 | 55% helix, 8% strand | P63208 |
| D | F-box only protein 31 | protein | 417 | 32% helix, 29% strand | Q5XUX0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 8 copies · chains B, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.84 | 0.92 | 53 | empty |
| 2 | 355 | 0.83 | 0.92 | 54 | empty |
| 3 | 78 | 0.73 | 0.96 | 19 | empty |
| 4 | 77 | 0.72 | 0.96 | 17 | empty |
| 5 | 228 | 0.51 | 0.76 | 38 | DTT |
Interfaces
3 interfaces between chains.
- A–B · 1619 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1603 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 251 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5VZT · Crystal structure of the Skp1-FBXO31 complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q5XUX0 · AlphaFold monomer V2.0 prediction for F-box only protein 31 (Q5XUX0) · a predicted model of the same protein · chain D against A, TM-score 1.00
- 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 0.94
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 Q5XUX0
- Elsewhere: RCSB PDB 5VZT · PDBe 5VZT · UniProt P63208 · UniProt Q5XUX0
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