MolNFT v1 · #47344 · protein

Structure of the SKP1-FBW7-cyclinedegc complex

2OVQ · S-phase kinase-associated protein 1A: “Structure of the SKP1-FBW7-cyclinedegc complex”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.79). MolNFT v1 #47344 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2OVQ
Type: protein
Length: 590 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 C-terminal degron
UniProt: P63208, Q969H0
Ligands: SO4
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S-phase kinase-associated protein 1A	protein	134	54% helix, 10% strand	P63208
B	F-BOX/WD repeat protein 7	protein	444	15% helix, 42% strand	Q969H0
C	Cycline C-terminal degron	protein	12	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	517	0.79	0.86	46	SO4
2	236	0.55	0.77	31	empty
3	77	0.39	0.78	19	empty
4	74	0.33	0.75	13	empty

Interfaces

2 interfaces between chains.

A–B · 1803 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 667 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

2OVQ · Structure of the Skp1-Fbw7-CyclinEdegC 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 0.93

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 2OVQ · PDBe 2OVQ · UniProt P63208 · UniProt Q969H0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.