Research workbench

Structure of the 26S proteasome-UBP6 complex in the si state (core particle and lid)

Analyse Structure of the 26S proteasome-UBP6 complex in the si state (core particle and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QO3
Type: protein
Length: 11,480 residues
Chains: 41
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome subunit alpha type-1; Proteasome subunit alpha type-2; Proteasome subunit…
EC: 3.4.25.1, 3.4.19.12
UniProt: P21243, P23639, P23638, P40303, P32379, P40302, P21242, P38624, P25043, P25451, P22141, P30656, P23724, P30657, P38886, P43588, P32496, O13563, O94742, P38764, P32565, P40016, Q12250, Q12377, Q06103, Q08723, Q04062
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 27 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a, A	Proteasome subunit alpha type-1	protein	241	37% helix, 22% strand	P21243
b, B	Proteasome subunit alpha type-2	protein	249	31% helix, 25% strand	P23639
c, C	Proteasome subunit alpha type-3	protein	244	37% helix, 25% strand	P23638
d, D	Proteasome subunit alpha type-4	protein	236	36% helix, 23% strand	P40303
e, E	Proteasome subunit alpha type-5	protein	244	32% helix, 25% strand	P32379
f, F	Proteasome subunit alpha type-6	protein	231	35% helix, 23% strand	P40302
g, G	Probable proteasome subunit alpha type-7	protein	242	37% helix, 26% strand	P21242
h, 1	Proteasome subunit beta type-1 (EC 3.4.25.1)	protein	196	35% helix, 30% strand	P38624
i, 2	Proteasome subunit beta type-2 (EC 3.4.25.1)	protein	226	29% helix, 32% strand	P25043
j, 3	Proteasome subunit beta type-3	protein	204	33% helix, 35% strand	P25451
k, 4	Proteasome subunit beta type-4	protein	195	34% helix, 34% strand	P22141
l, 5	Proteasome subunit beta type-5 (EC 3.4.25.1)	protein	212	36% helix, 34% strand	P30656
m, 6	Proteasome subunit beta type-6	protein	222	29% helix, 30% strand	P23724
n, 7	Proteasome subunit beta type-7	protein	229	31% helix, 31% strand	P30657
W	26S proteasome regulatory subunit RPN10	protein	197	36% helix, 18% strand	P38886
V	Ubiquitin carboxyl-terminal hydrolase RPN11 (EC 3.4.19.12)	protein	289	43% helix, 19% strand	P43588
T	26S proteasome regulatory subunit RPN12	protein	266	71% helix, 2% strand	P32496
X	26S proteasome regulatory subunit RPN13	protein	127	9% helix, 29% strand	O13563
Y	26S proteasome complex subunit SEM1	protein	89	51% helix, 0% strand	O94742
Z	26S proteasome regulatory subunit RPN1	protein	906	60% helix, 2% strand	P38764
N	26S proteasome regulatory subunit RPN2	protein	832	64% helix, 3% strand	P32565
S	26S proteasome regulatory subunit RPN3	protein	475	70% helix, 2% strand	P40016
P	26S proteasome regulatory subunit RPN5	protein	440	73% helix, 3% strand	Q12250
Q	26S proteasome regulatory subunit RPN6	protein	434	71% helix, 2% strand	Q12377
R	26S proteasome regulatory subunit RPN7	protein	405	71% helix, 3% strand	Q06103
U	26S proteasome regulatory subunit RPN8	protein	290	47% helix, 20% strand	Q08723
O	26S proteasome regulatory subunit RPN9	protein	388	72% helix, 4% strand	Q04062

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	655	0.86	0.90	78	empty
2	920	0.83	0.85	124	empty
3	491	0.83	0.89	70	empty
4	614	0.79	0.84	53	empty
5	899	0.78	0.81	87	empty

Interfaces

125 interfaces between chains.

V–U · 3873 Å² buried · 36 hydrogen bonds · protein-protein
Y–S · 2789 Å² buried · 28 hydrogen bonds · protein-protein
T–S · 2384 Å² buried · 14 hydrogen bonds · protein-protein
U–O · 2098 Å² buried · 17 hydrogen bonds · protein-protein
2–3 · 1796 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

7QO3 · Structure of the 26S proteasome-Ubp6 complex in the si state (Core Particle and Lid) · the same entry in another collection · chain k against k, TM-score 1.00

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 P21243
Every structure of UniProt P23639
Every structure of UniProt P23638
Every structure of UniProt P40303
Every structure of UniProt P32379
Every structure of UniProt P40302
Every structure of UniProt P21242
Every structure of UniProt P38624
Every structure of UniProt P25043
Every structure of UniProt P25451
Every structure of UniProt P22141
Every structure of UniProt P30656
Every structure of UniProt P23724
Every structure of UniProt P30657
Every structure of UniProt P38886
Every structure of UniProt P43588
Every structure of UniProt P32496
Every structure of UniProt O13563
Every structure of UniProt O94742
Every structure of UniProt P38764
Every structure of UniProt P32565
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
Elsewhere: RCSB PDB 7QO3 · PDBe 7QO3 · UniProt P21243 · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P38624 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · UniProt P38886 · UniProt P43588 · UniProt P32496 · UniProt O13563 · UniProt O94742 · UniProt P38764 · UniProt P32565 · UniProt P40016 · UniProt Q12250 · UniProt Q12377 · UniProt Q06103 · UniProt Q08723 · UniProt Q04062

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