MolNFT v1 · #173621 · protein

Ubiquitin ligation to F-box protein substrates by scf-rbr E3-E3 super- assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-cyclin a-CDK2-P27

7B5R · Cullin-1: “Ubiquitin ligation to F-box protein substrates by scf-rbr E3-E3 super- assembly…”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #173621 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7B5R
Type: protein
Length: 1,430 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cullin-1; S-phase kinase-associated protein 2; Cyclin-dependent kinases regulatory…
EC: 2.7.11.22
UniProt: Q13616, Q13309, P61024, P63208, P24941, P20248, P46527
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 7 distinct chains · 47% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Cullin-1	protein	288	71% helix, 0% strand	Q13616
T	S-phase kinase-associated protein 2	protein	321	32% helix, 9% strand	Q13309
K	Cyclin-dependent kinases regulatory subunit 1	protein	69	16% helix, 26% strand	P61024
S	S-phase kinase-associated protein 1	protein	138	53% helix, 8% strand	P63208
L	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	284	33% helix, 10% strand	P24941
Y	Cyclin-A2	protein	253	65% helix, 0% strand	P20248
P	Cyclin-dependent kinase inhibitor 1B	protein	77	27% helix, 3% strand	P46527

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	201	0.79	0.93	30	empty
2	85	0.76	0.98	24	empty
3	629	0.73	0.80	73	empty
4	515	0.70	0.80	76	empty
5	147	0.68	0.89	29	empty

Interfaces

11 interfaces between chains.

L–P · 1619 Å² buried · 20 hydrogen bonds · protein-protein
L–Y · 1520 Å² buried · 14 hydrogen bonds · protein-protein
T–S · 1446 Å² buried · 6 hydrogen bonds · protein-protein
Y–P · 978 Å² buried · 8 hydrogen bonds · protein-protein
T–K · 811 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

7B5R · Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly… · the same entry in another collection · chain P against P, TM-score 1.00
P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain Y against A, TM-score 0.98
Q13309 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 2 (Q13309) · a predicted model of the same protein · chain T against A, TM-score 0.98
Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain C against A, TM-score 0.95
P61024 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinases regulatory subunit 1… · a predicted model of the same protein · chain K against A, TM-score 0.95
P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain L against A, TM-score 0.88

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 Q13309
Every structure of UniProt P61024
Every structure of UniProt P63208
Every structure of UniProt P24941
Every structure of UniProt P20248
Every structure of UniProt P46527
Elsewhere: RCSB PDB 7B5R · PDBe 7B5R · UniProt Q13616 · UniProt Q13309 · UniProt P61024 · UniProt P63208 · UniProt P24941 · UniProt P20248 · UniProt P46527

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