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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: 2DZN
Type: protein
Length: 873 residues
Chains: 6
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 · 5 distinct chains · 54% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable 26S proteasome regulatory subunit P28	protein	226	51% helix, 1% strand	P50086
B	26S protease regulatory subunit 6B homolog	protein	57	46% helix, 7% strand	P33298
C, E	Probable 26S proteasome regulatory subunit P28	protein	227	55% helix, 1% strand	P50086
D	26S protease regulatory subunit 6B homolog	protein	67	61% helix, 3% strand	P33298
F	26S protease regulatory subunit 6B homolog	protein	69	61% helix, 3% strand	P33298

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1091	0.70	0.74	91	empty
2	199	0.53	0.78	33	empty
3	84	0.48	0.82	15	empty
4	95	0.45	0.80	23	empty
5	103	0.37	0.74	16	empty

Interfaces

7 interfaces between chains.

E–F · 1229 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1164 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 971 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 396 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 278 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2DZN · Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3 · the same entry in another collection · chain F against F, 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 A 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 0.92

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

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