MolNFT v1 · #83413 · protein

Crystal structure of pan-RPT5C chimera

3WHK · Proteasome-activating nucleotidase, 26S protease regulatory…: “Crystal structure of pan-RPT5C chimera”. X-ray diffraction, 1 ligand (ATP), 20 pockets (best druggability 0.70). MolNFT v1 #83413 on GenesisL1: 3D structure, binding…

PDB: 3WHK
Type: protein
Length: 1,964 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
UniProt: Q8U4H3, P33297
Ligands: ATP
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	248	48% helix, 14% strand	Q8U4H3, P33297
B, F	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	244	48% helix, 14% strand	Q8U4H3, P33297
C, G	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	245	49% helix, 14% strand	Q8U4H3, P33297
D	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	245	49% helix, 14% strand	Q8U4H3, P33297
E	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	247	49% helix, 14% strand	Q8U4H3, P33297
H	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A	protein	246	48% helix, 14% strand	Q8U4H3, P33297

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 8 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

20 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	1090	0.70	0.75	123	ATP
2	591	0.67	0.77	78	ATP
3	493	0.64	0.77	63	empty
4	419	0.63	0.77	49	empty
5	254	0.58	0.78	25	empty

Interfaces

11 interfaces between chains.

C–D · 1019 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 990 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 976 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 971 Å² buried · 15 hydrogen bonds · protein-protein
C–F · 287 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3WHK · Crystal structure of PAN-Rpt5C chimera · the same entry in another collection · chain B against B, TM-score 1.00
Q8U4H3 · AlphaFold monomer V2.0 prediction for proteasome-activating nucleotidase (Q8U4H3) · a predicted model of the same protein · chain D against A, TM-score 0.95

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
Elsewhere: RCSB PDB 3WHK · PDBe 3WHK · UniProt Q8U4H3 · UniProt P33297

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