Research workbench

26S proteasome in presence of ATP (S1)

Analyse 26S proteasome in presence of ATP (S1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MPD
Type: protein
Length: 5,142 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26S proteasome regulatory subunit RPN10; Ubiquitin carboxyl-terminal hydrolase RPN11; 26S…
EC: 3.4.19.12
UniProt: P38886, P43588, P32496, O13563, O94742, P38764, P32565, P40016, Q12250, Q12377, Q06103, Q08723, Q04062
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 13 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
W	26S proteasome regulatory subunit RPN10	protein	197	32% helix, 19% strand	P38886
V	Ubiquitin carboxyl-terminal hydrolase RPN11 (EC 3.4.19.12)	protein	289	46% helix, 16% strand	P43588
T	26S proteasome regulatory subunit RPN12	protein	266	71% helix, 1% strand	P32496
X	26S proteasome regulatory subunit RPN13	protein	127	9% helix, 25% strand	O13563
Y	26S proteasome complex subunit SEM1	protein	51	67% helix, 0% strand	O94742
Z	26S proteasome regulatory subunit RPN1	protein	906	61% helix, 3% strand	P38764
N	26S proteasome regulatory subunit RPN2	protein	890	64% helix, 4% strand	P32565
S	26S proteasome regulatory subunit RPN3	protein	475	69% helix, 3% strand	P40016
P	26S proteasome regulatory subunit RPN5	protein	440	74% helix, 2% strand	Q12250
Q	26S proteasome regulatory subunit RPN6	protein	434	74% helix, 3% strand	Q12377
R	26S proteasome regulatory subunit RPN7	protein	381	76% helix, 3% strand	Q06103
U	26S proteasome regulatory subunit RPN8	protein	298	48% helix, 20% strand	Q08723
O	26S proteasome regulatory subunit RPN9	protein	388	72% helix, 3% 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	348	0.82	0.92	45	empty
2	643	0.81	0.86	82	empty
3	1007	0.81	0.82	86	empty
4	1088	0.81	0.82	89	empty
5	231	0.77	0.90	38	empty

Interfaces

31 interfaces between chains.

V–U · 3996 Å² buried · 19 hydrogen bonds · protein-protein
T–S · 2062 Å² buried · 20 hydrogen bonds · protein-protein
Y–S · 1643 Å² buried · 22 hydrogen bonds · protein-protein
U–O · 1587 Å² buried · 4 hydrogen bonds · protein-protein
P–U · 1343 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5MPD · 26S proteasome in presence of ATP (s1) · the same entry in another collection · chain R against R, 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 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 5MPD · PDBe 5MPD · 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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