MolNFT v1 · #179389 · protein

Bacterial O-glcnacase (oga) with compound

7K41 · O-glcnacase BT_4395: “Bacterial O-glcnacase (oga) with compound”. X-ray diffraction, 1 ligand (VUA), 10 pockets (best druggability 0.61). MolNFT v1 #179389 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K41
Type: protein
Length: 590 residues
Chains: 1
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: VUA
Pockets: 10 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glcnacase BT_4395 (EC 3.2.1.169)	protein	590	46% helix, 15% strand	Q89ZI2

Ligands and binding sites

VUA · 4-(4-methylpiperidin-1-yl)-N-(2-phenylethyl)pyrimidin-2-amine · ligand · chains A
EDO · 1,2-ethanediol · additive · 10 copies · chains A
ACT · Acetate ion · additive · 2 copies · chains A

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	219	0.61	0.81	33	VUA, EDO
2	65	0.50	0.85	15	empty
3	113	0.44	0.78	25	empty
4	142	0.44	0.76	29	ACT
5	124	0.39	0.74	19	EDO

Compared structures

7K41 · Bacterial O-GlcNAcase (OGA) with compound · the same entry in another collection · 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 7K41 · PDBe 7K41 · UniProt Q89ZI2

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