MolNFT v1 · #34981 · protein

Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome

2DWZ · 26S proteasome non-ATPase regulatory subunit 10: “Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome”. X-ray diffraction, 7 pockets (best druggability 0.52). MolNFT v1 #34981 on GenesisL1: 3D…

PDB: 2DWZ
Type: protein
Length: 598 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26S proteasome non-ATPase regulatory subunit 10; 26S protease regulatory subunit 6B
UniProt: Q9Z2X2, Q63570
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	26S proteasome non-ATPase regulatory subunit 10	protein	226	53% helix, 0% strand	Q9Z2X2
B, D	26S protease regulatory subunit 6B	protein	73	59% helix, 3% strand	Q63570

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

7 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	200	0.52	0.77	19	empty
2	149	0.52	0.80	22	empty
3	123	0.46	0.78	21	empty
4	123	0.43	0.77	28	empty
5	88	0.33	0.73	15	empty

Interfaces

3 interfaces between chains.

A–B · 1269 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1255 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 738 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2DWZ · Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome · the same entry in another collection · chain A against A, TM-score 1.00
Q9Z2X2 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 10… · a predicted model of the same protein · chain A against A, TM-score 0.99
Q63570 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 6B (Q63570) · a predicted model of the same protein · chain B 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 Q9Z2X2
Every structure of UniProt Q63570
Elsewhere: RCSB PDB 2DWZ · PDBe 2DWZ · UniProt Q9Z2X2 · UniProt Q63570

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