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Structure of the CUL1-RBX1-SKP1-F BOXSKP2 scf ubiquitin ligase complex

Analyse Structure of the CUL1-RBX1-SKP1-F BOXSKP2 scf ubiquitin ligase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LDK
Type: protein
Length: 971 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cullin homolog; Ring-box protein 1; Cyclin A/CDK2-associated protein P19; SKP2-like…
UniProt: Q13616, P62877, P63208, Q13309
Ligands: ZN
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 50% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cullin homolog	protein	358	70% helix, 0% strand	Q13616
B	Cullin homolog	protein	366	41% helix, 6% strand	Q13616
C	Ring-box protein 1	protein	88	5% helix, 15% strand	P62877
D	Cyclin A/CDK2-associated protein P19	protein	118	52% helix, 3% strand	P63208
E	SKP2-like protein type gamma	protein	41	51% helix, 0% strand	Q13309

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains C

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	518	0.77	0.84	63	empty
2	467	0.75	0.84	45	empty
3	381	0.69	0.81	59	empty
4	228	0.68	0.85	31	empty
5	78	0.56	0.86	27	empty

Interfaces

5 interfaces between chains.

B–C · 2433 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 966 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 767 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 724 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 302 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

1LDK · Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex · the same entry in another collection · chain E against E, TM-score 1.00
Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain A against A, TM-score 0.97
P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain D against A, TM-score 0.94
Q13309 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 2 (Q13309) · a predicted model of the same protein · chain E against A, TM-score 0.82
P62877 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RBX1 (P62877) · a predicted model of the same protein · chain C against A, TM-score 0.57

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 Q13616
Every structure of UniProt P62877
Every structure of UniProt P63208
Every structure of UniProt Q13309
Elsewhere: RCSB PDB 1LDK · PDBe 1LDK · UniProt Q13616 · UniProt P62877 · UniProt P63208 · UniProt Q13309

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