Research workbench

Structure of the FBW7-SKP1-mycndegron complex

Analyse Structure of the FBW7-SKP1-mycndegron complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7T1Z
Type: protein
Length: 579 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S-phase kinase-associated protein 1; F-BOX/WD repeat-containing protein 7; Myc…
UniProt: P63208, Q969H0
Ligands: SO4
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S-phase kinase-associated protein 1	protein	129	51% helix, 8% strand	P63208
B	F-BOX/WD repeat-containing protein 7	protein	438	13% helix, 43% strand	Q969H0
C	Myc proto-oncogene N terminal degron	protein	12	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	591	0.79	0.85	63	SO4
2	84	0.38	0.77	17	empty
3	85	0.36	0.75	15	empty

Interfaces

2 interfaces between chains.

A–B · 1803 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 784 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

7T1Z · Structure of the Fbw7-Skp1-MycNdegron 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

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 7T1Z · PDBe 7T1Z · UniProt P63208 · UniProt Q969H0

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