Research workbench

BTGH84 in complex with 6-acetamido-6-deoxy-castanospermine

Analyse BTGH84 in complex with 6-acetamido-6-deoxy-castanospermine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XJ7
Type: protein
Length: 1,272 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: GC2, CA
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glcnacase BT_4395 (EC 3.2.1.52)	protein	639	43% helix, 18% strand	Q89ZI2
B	O-glcnacase BT_4395 (EC 3.2.1.52)	protein	633	43% helix, 18% strand	Q89ZI2

Ligands and binding sites

GC2 · 6-acetamido-6-deoxy-castanospermine · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

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	470	0.68	0.79	48	empty
2	410	0.63	0.77	55	empty
3	83	0.59	0.87	18	GC2
4	267	0.57	0.77	34	empty
5	231	0.56	0.78	30	empty

Interfaces

1 interface between chains.

A–B · 1067 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

2XJ7 · BtGH84 in complex with 6-acetamido-6-deoxy-castanospermine · the same entry in another collection · chain A against A, TM-score 1.00
Q89ZI2 · AlphaFold monomer V2.0 prediction for O-glcnacase BT_4395 (Q89ZI2) · a predicted model of the same protein · chain B 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 2XJ7 · PDBe 2XJ7 · UniProt Q89ZI2

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