MolNFT v1 · #32252 · protein

NEDD8 protease

2BKQ · Sentrin-specific protease 8: “NEDD8 protease”. X-ray diffraction, 6 pockets (best druggability 0.80). MolNFT v1 #32252 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2BKQ
Type: protein
Length: 834 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sentrin-specific protease 8
EC: 3.4.22.-
UniProt: Q96LD8
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sentrin-specific protease 8 (EC 3.4.22.-)	protein	210	49% helix, 18% strand	Q96LD8
B	Sentrin-specific protease 8 (EC 3.4.22.-)	protein	208	52% helix, 17% strand	Q96LD8
C	Sentrin-specific protease 8 (EC 3.4.22.-)	protein	207	50% helix, 17% strand	Q96LD8
D	Sentrin-specific protease 8 (EC 3.4.22.-)	protein	209	50% helix, 18% strand	Q96LD8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1135	0.80	0.81	122	empty
2	174	0.45	0.75	27	empty
3	142	0.42	0.74	25	empty
4	109	0.38	0.75	19	empty
5	65	0.37	0.79	22	empty

Interfaces

2 interfaces between chains.

A–C · 639 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 358 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2BKQ · NEDD8 protease · the same entry in another collection · chain D against D, TM-score 1.00
Q96LD8 · AlphaFold monomer V2.0 prediction for sentrin-specific protease 8 (Q96LD8) · a predicted model of the same protein · chain C 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 Q96LD8
Elsewhere: RCSB PDB 2BKQ · PDBe 2BKQ · UniProt Q96LD8

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