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Crystal structure of NAS2 N-terminal domain complexed with pan-RPT5C chimera

Analyse Crystal structure of NAS2 N-terminal domain complexed with pan-RPT5C chimera in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WHL
Type: protein
Length: 1,296 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A; Probable 26S…
UniProt: Q8U4H3, P33297, P40555
Ligands: ATP
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 7 distinct chains · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	237	47% helix, 16% strand	Q8U4H3, P33297
B, D	Probable 26S proteasome regulatory subunit P27	protein	92	76% helix, 0% strand	P40555
C	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	232	49% helix, 15% strand	Q8U4H3, P33297
E	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	228	50% helix, 15% strand	Q8U4H3, P33297
F	Probable 26S proteasome regulatory subunit P27	protein	90	71% helix, 0% strand	P40555
G	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	234	48% helix, 15% strand	Q8U4H3, P33297
H	Probable 26S proteasome regulatory subunit P27	protein	91	74% helix, 0% strand	P40555

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	996	0.74	0.77	92	ATP
2	1006	0.71	0.75	85	ATP
3	608	0.70	0.79	71	ATP
4	825	0.70	0.76	62	ATP
5	743	0.70	0.77	80	empty

Interfaces

11 interfaces between chains.

C–E · 1005 Å² buried · 12 hydrogen bonds · protein-protein
A–G · 950 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 827 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 813 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 747 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3WHL · Crystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera · the same entry in another collection · chain A against A, TM-score 1.00
Q8U4H3 · AlphaFold monomer V2.0 prediction for proteasome-activating nucleotidase (Q8U4H3) · a predicted model of the same protein · chain G against A, TM-score 0.96

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 Q8U4H3
Every structure of UniProt P33297
Every structure of UniProt P40555
Elsewhere: RCSB PDB 3WHL · PDBe 3WHL · UniProt Q8U4H3 · UniProt P33297 · UniProt P40555

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