MolNFT v1 · #47345 · protein
Structure of the SKP1-FBW7-cyclinedegn complex
2OVR · S-phase kinase-associated protein 1A: “Structure of the SKP1-FBW7-cyclinedegn complex”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.79). MolNFT v1 #47345 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2OVR
- Type
- protein
- Length
- 586 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-phase kinase-associated protein 1A; F-BOX/WD repeat protein 7; Cycline N-terminal degron
- UniProt
- P63208, Q969H0
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-phase kinase-associated protein 1A | protein | 136 | 54% helix, 10% strand | P63208 |
| B | F-BOX/WD repeat protein 7 | protein | 442 | 14% helix, 42% strand | Q969H0 |
| C | Cycline N-terminal degron | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.79 | 0.85 | 53 | SO4 |
| 2 | 220 | 0.55 | 0.78 | 32 | empty |
| 3 | 99 | 0.39 | 0.76 | 15 | empty |
| 4 | 74 | 0.37 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1822 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 469 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 2OVR · Structure of the Skp1-Fbw7-CyclinEdegN complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q969H0 · AlphaFold monomer V2.0 prediction for F-BOX/WD repeat-containing protein 7 (Q969H0) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain A 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 Q969H0
- Elsewhere: RCSB PDB 2OVR · PDBe 2OVR · UniProt P63208 · UniProt Q969H0
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