Research workbench

Conformational landscape of the P28-bound human proteasome regulatory particle

Analyse Conformational landscape of the P28-bound human proteasome regulatory particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VHP
Type: protein
Length: 2,265 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26S proteasome non-ATPase regulatory subunit 10; 26S proteasome regulatory subunit 7; 26S…
UniProt: O75832, P35998, P62191, P43686, P62333, P17980, P62195, Q13200
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 8 distinct chains · 50% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	26S proteasome non-ATPase regulatory subunit 10	protein	224	54% helix, 0% strand	O75832
A	26S proteasome regulatory subunit 7	protein	258	45% helix, 7% strand	P35998
B	26S proteasome regulatory subunit 4	protein	227	49% helix, 10% strand	P62191
D	26S proteasome regulatory subunit 6B	protein	237	39% helix, 7% strand	P43686
E	26S proteasome regulatory subunit 10B	protein	209	43% helix, 11% strand	P62333
F	26S proteasome regulatory subunit 6A	protein	238	47% helix, 8% strand	P17980
C	26S proteasome regulatory subunit 8	protein	236	41% helix, 9% strand	P62195
f	26S proteasome non-ATPase regulatory subunit 2	protein	636	62% helix, 0% strand	Q13200

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	770	0.85	0.88	101	empty
2	1000	0.83	0.84	124	empty
3	489	0.81	0.88	67	empty
4	550	0.81	0.87	88	empty
5	928	0.81	0.83	107	empty

Interfaces

8 interfaces between chains.

E–F · 1824 Å² buried · 22 hydrogen bonds · protein-protein
G–D · 1235 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1143 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 1049 Å² buried · 8 hydrogen bonds · protein-protein
D–C · 505 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5VHP · Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle · the same entry in another collection · chain f against f, TM-score 1.00
O75832 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 10… · a predicted model of the same protein · chain G against A, TM-score 0.96
Q13200 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 2… · a predicted model of the same protein · chain f against A, TM-score 0.88
P62333 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 10B (P62333) · a predicted model of the same protein · chain E against A, TM-score 0.86
P43686 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 6B (P43686) · a predicted model of the same protein · chain D against A, TM-score 0.81

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 O75832
Every structure of UniProt P35998
Every structure of UniProt P62191
Every structure of UniProt P43686
Every structure of UniProt P62333
Every structure of UniProt P17980
Every structure of UniProt P62195
Every structure of UniProt Q13200
Elsewhere: RCSB PDB 5VHP · PDBe 5VHP · UniProt O75832 · UniProt P35998 · UniProt P62191 · UniProt P43686 · UniProt P62333 · UniProt P17980 · UniProt P62195 · UniProt Q13200

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