Research workbench

Crystal structure of the SKP1-SKP2-CKS1 complex

Analyse Crystal structure of the SKP1-SKP2-CKS1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ASS
Type: protein
Length: 537 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S-phase kinase-associated protein 1A; S-phase kinase-associated protein 2…
UniProt: P63208, Q13309, P61024
Ligands: BEN, PO4
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S-phase kinase-associated protein 1A	protein	143	49% helix, 8% strand	P63208
B	S-phase kinase-associated protein 2	protein	325	30% helix, 14% strand	Q13309
C	Cyclin-dependent kinases regulatory subunit 1	protein	69	14% helix, 33% strand	P61024

Ligands and binding sites

BEN · Benzamidine · ligand · 2 copies · chains B, C
PO4 · Phosphate ion · ion · 3 copies · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 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	444	0.65	0.78	61	PO4, BEN
2	83	0.58	0.88	25	empty
3	68	0.33	0.76	13	empty
4	68	0.31	0.74	18	empty
5	59	0.27	0.73	19	empty

Interfaces

2 interfaces between chains.

A–B · 1546 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 918 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

2ASS · Crystal structure of the Skp1-Skp2-Cks1 complex · the same entry in another collection · chain A against A, TM-score 1.00
Q13309 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 2 (Q13309) · a predicted model of the same protein · chain B against A, TM-score 0.99
P61024 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinases regulatory subunit 1… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 0.92

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 Q13309
Every structure of UniProt P61024
Elsewhere: RCSB PDB 2ASS · PDBe 2ASS · UniProt P63208 · UniProt Q13309 · UniProt P61024

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