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Structure of ligand bound glycosylhydrolase

Analyse Structure of ligand bound glycosylhydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UR9
Type: protein
Length: 1,352 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase BT_4395
EC: 3.2.1.169
UniProt: Q89ZI2
Ligands: BK9, OAN, CA
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glcnacase BT_4395 (EC 3.2.1.169)	protein	685	39% helix, 20% strand	Q89ZI2
B	O-glcnacase BT_4395 (EC 3.2.1.169)	protein	667	39% helix, 19% strand	Q89ZI2

Ligands and binding sites

BK9 · 4-ethoxyquinazoline · ligand · 2 copies · chains A, B
OAN · O-(2-acetamido-2-deoxy D-glucopyranosylidene) amino-N-phenylcarbamate · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · chains 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	598	0.70	0.78	47	empty
2	472	0.65	0.78	63	empty
3	261	0.61	0.80	29	empty
4	270	0.56	0.77	26	empty
5	105	0.55	0.83	21	BK9, OAN

Interfaces

1 interface between chains.

A–B · 1105 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4UR9 · Structure of ligand bound glycosylhydrolase · 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 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 4UR9 · PDBe 4UR9 · UniProt Q89ZI2

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