MolNFT v1 · #137806 · protein
Crystal structure of the SKP1-FBXO31-cyclin D1 complex
5VZU · S-phase kinase-associated protein 1: “Crystal structure of the SKP1-FBXO31-cyclin D1 complex”. X-ray diffraction, 2 ligands (ZN, PO4), 11 pockets (best druggability 0.83). MolNFT v1 #137806 on GenesisL1: 3D structure, binding sites…
- PDB
- 5VZU
- Type
- protein
- Length
- 1,138 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-phase kinase-associated protein 1; F-box only protein 31; Cyclin D1
- UniProt
- P63208, Q5XUX0, Q9H014
- Ligands
- ZN, PO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-phase kinase-associated protein 1 | protein | 145 | 57% helix, 8% strand | P63208 |
| B | F-box only protein 31 | protein | 418 | 32% helix, 32% strand | Q5XUX0 |
| C | S-phase kinase-associated protein 1 | protein | 143 | 57% helix, 8% strand | P63208 |
| D | F-box only protein 31 | protein | 417 | 32% helix, 32% strand | Q5XUX0 |
| E | Cyclin D1 | protein | 9 | 67% helix, 0% strand | Q9H014 |
| F | Cyclin D1 | protein | 6 | 50% helix, 0% strand | Q9H014 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.83 | 0.92 | 49 | empty |
| 2 | 407 | 0.83 | 0.91 | 53 | empty |
| 3 | 62 | 0.70 | 0.96 | 18 | empty |
| 4 | 204 | 0.49 | 0.75 | 33 | empty |
| 5 | 98 | 0.37 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1593 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1562 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 508 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 428 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 254 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VZU · Crystal structure of the Skp1-FBXO31-cyclin D1 complex · the same entry in another collection · chain F against F, 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 0.95
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
- Every structure of UniProt Q9H014
- Elsewhere: RCSB PDB 5VZU · PDBe 5VZU · UniProt P63208 · UniProt Q5XUX0 · UniProt Q9H014
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