Research workbench

Structure of the yeast 26S proteasome lid sub-complex

Analyse Structure of the yeast 26S proteasome lid sub-complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JCK
Type: protein
Length: 2,777 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26S proteasome regulatory subunit RPN3; 26S proteasome regulatory subunit RPN5; 26S…
EC: 3.4.19.12
UniProt: P40016, Q12250, Q12377, Q06103, Q08723, Q04062, P43588, P32496, O94742
Ligands: ZN
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 9 distinct chains · 67% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	26S proteasome regulatory subunit RPN3	protein	397	70% helix, 3% strand	P40016
B	26S proteasome regulatory subunit RPN5	protein	404	73% helix, 3% strand	Q12250
C	26S proteasome regulatory subunit RPN6	protein	378	72% helix, 3% strand	Q12377
D	26S proteasome regulatory subunit RPN7	protein	384	74% helix, 4% strand	Q06103
E	26S proteasome regulatory subunit RPN8	protein	277	48% helix, 17% strand	Q08723
F	26S proteasome regulatory subunit RPN9	protein	388	72% helix, 3% strand	Q04062
G	Ubiquitin carboxyl-terminal hydrolase RPN11 (EC 3.4.19.12)	protein	257	45% helix, 17% strand	P43588
H	26S proteasome regulatory subunit RPN12	protein	246	70% helix, 3% strand	P32496
I	26S proteasome complex subunit SEM1	protein	46	41% helix, 0% strand	O94742

Ligands and binding sites

ZN · Zinc ion · metal · chains B, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	447	0.79	0.87	64	empty
2	771	0.79	0.83	77	empty
3	1163	0.78	0.80	115	empty
4	699	0.74	0.80	70	empty
5	911	0.73	0.77	65	empty

Interfaces

20 interfaces between chains.

E–G · 3503 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1895 Å² buried · 15 hydrogen bonds · protein-protein
A–H · 1837 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1416 Å² buried · 17 hydrogen bonds · protein-protein
B–G · 1397 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3JCK · Structure of the yeast 26S proteasome lid sub-complex · the same entry in another collection · chain I against I, TM-score 1.00
Q06103 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN7 (Q06103) · a predicted model of the same protein · chain D against A, TM-score 0.93
Q12250 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN5 (Q12250) · a predicted model of the same protein · chain B against A, TM-score 0.92
Q04062 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN9 (Q04062) · a predicted model of the same protein · chain F 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 P40016
Every structure of UniProt Q12250
Every structure of UniProt Q12377
Every structure of UniProt Q06103
Every structure of UniProt Q08723
Every structure of UniProt Q04062
Every structure of UniProt P43588
Every structure of UniProt P32496
Every structure of UniProt O94742
Elsewhere: RCSB PDB 3JCK · PDBe 3JCK · UniProt P40016 · UniProt Q12250 · UniProt Q12377 · UniProt Q06103 · UniProt Q08723 · UniProt Q04062 · UniProt P43588 · UniProt P32496 · UniProt O94742

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