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Structure of human O-glcnac hydrolase with pugnac type inhibitor

Analyse Structure of human O-glcnac hydrolase with pugnac type inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M7T
Type: protein
Length: 898 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein O-glcnacase
EC: 3.2.1.169, 3.2.1.-
UniProt: O60502
Ligands: GDV
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-)	protein	451	49% helix, 9% strand	O60502
B	Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-)	protein	447	49% helix, 9% strand	O60502

Ligands and binding sites

GDV · (5R,6R,7R,8S)-8-(acetylamino)-6,7-dihydroxy-5-(hydroxymethyl)-N-phenyl-1,5,6,7,8,8A-hexahydroimidazo[1,2-a]pyridine-2-carboxamide · ligand · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.83	0.84	82	empty
2	476	0.68	0.79	40	GDV
3	424	0.66	0.79	41	GDV
4	92	0.58	0.87	17	empty
5	67	0.35	0.77	13	empty

Interfaces

1 interface between chains.

A–B · 4380 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

5M7T · Structure of human O-GlcNAc hydrolase with PugNAc type inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
O60502 · AlphaFold monomer V2.0 prediction for protein O-glcnacase (O60502) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 O60502
Elsewhere: RCSB PDB 5M7T · PDBe 5M7T · UniProt O60502

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