MolNFT v1 · #41289 · protein

Bacteroides thetaiotaomicron GH84 O-glcnacase in complex with 2-acetylamino-2-deoxy-1-epivalienamine

2JIW · O-glcnacase BT_4395: “Bacteroides thetaiotaomicron GH84 O-glcnacase in complex with 2-acetylamino-2-deoxy-1-epivalienamine”. X-ray diffraction, 1 ligand (BEU), 15 pockets (best druggability 0.58). MolNFT v1 #41289 on GenesisL1: 3D…

PDB: 2JIW
Type: protein
Length: 1,180 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase BT_4395
EC: 3.2.1.52
UniProt: Q89ZI2
Ligands: BEU
Pockets: 15 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	O-glcnacase BT_4395 (EC 3.2.1.52)	protein	590	45% helix, 14% strand	Q89ZI2

Ligands and binding sites

BEU · N-[(1S,2R,5R,6R)-2-amino-5,6-dihydroxy-4-(hydroxymethyl)cyclohex-3-en-1-yl]acetamide · ligand · 2 copies · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	346	0.58	0.76	36	empty
2	86	0.57	0.86	19	BEU
3	81	0.51	0.84	20	BEU
4	106	0.48	0.80	18	empty
5	119	0.45	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 379 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2JIW · Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2… · the same entry in another collection · chain B against B, TM-score 1.00
Q89ZI2 · AlphaFold monomer V2.0 prediction for O-glcnacase BT_4395 (Q89ZI2) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q89ZI2
Elsewhere: RCSB PDB 2JIW · PDBe 2JIW · UniProt Q89ZI2

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