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Crystal structure analysis of yeast NAS6P complexed with the proteasome subunit, RPT3

Analyse Crystal structure analysis of yeast NAS6P complexed with the proteasome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DZO
Type: protein
Length: 579 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable 26S proteasome regulatory subunit P28; 26S protease regulatory subunit 6B homolog
UniProt: P50086, P33298
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable 26S proteasome regulatory subunit P28	protein	228	50% helix, 1% strand	P50086
B	26S protease regulatory subunit 6B homolog	protein	57	56% helix, 4% strand	P33298
C	Probable 26S proteasome regulatory subunit P28	protein	227	48% helix, 0% strand	P50086
D	26S protease regulatory subunit 6B homolog	protein	67	57% helix, 3% strand	P33298

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	765	0.70	0.77	83	empty
2	164	0.55	0.81	37	empty
3	80	0.51	0.84	15	empty
4	173	0.48	0.76	32	empty
5	59	0.38	0.80	13	empty

Interfaces

6 interfaces between chains.

C–D · 1136 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1005 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 393 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 311 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 187 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2DZO · Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3 · the same entry in another collection · chain D against D, TM-score 1.00
P50086 · AlphaFold monomer V2.0 prediction for probable 26S proteasome regulatory subunit P28… · a predicted model of the same protein · chain C against A, TM-score 0.99
P33298 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 6B homolog… · a predicted model of the same protein · chain D against A, TM-score 0.91

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 P50086
Every structure of UniProt P33298
Elsewhere: RCSB PDB 2DZO · PDBe 2DZO · UniProt P50086 · UniProt P33298

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