MolNFT v1 · #179846 · protein

Ogoga in complex with ligand 55

7KHS · Protein O-glcnacase: “Ogoga in complex with ligand 55”. X-ray diffraction, 2 ligands (WG4, CA), 20 pockets (best druggability 0.83). MolNFT v1 #179846 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KHS
Type: protein
Length: 1,754 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein O-glcnacase
EC: 3.2.1.169
UniProt: Q2CEE3
Ligands: WG4, CA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein O-glcnacase (EC 3.2.1.169)	protein	449	49% helix, 11% strand	Q2CEE3
B	Protein O-glcnacase (EC 3.2.1.169)	protein	430	49% helix, 11% strand	Q2CEE3
C	Protein O-glcnacase (EC 3.2.1.169)	protein	427	49% helix, 12% strand	Q2CEE3
D	Protein O-glcnacase (EC 3.2.1.169)	protein	448	49% helix, 11% strand	Q2CEE3

Ligands and binding sites

WG4 · N-(5-{[(5S)-7-(5-methylimidazo[1,2-a]pyrimidin-7-yl)-2, 7-diazaspiro[4.4]nonan-2-yl]methyl}-1,3-thiazol-2-yl) acetamide · ligand · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1061	0.83	0.84	90	WG4
2	735	0.81	0.85	55	empty
3	579	0.78	0.85	75	EDO
4	75	0.74	0.98	22	empty
5	694	0.72	0.79	58	WG4

Interfaces

3 interfaces between chains.

A–B · 3828 Å² buried · 40 hydrogen bonds · protein-protein
C–D · 3774 Å² buried · 38 hydrogen bonds · protein-protein
A–D · 408 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7KHS · OgOGA IN COMPLEX WITH LIGAND 55 · the same entry in another collection · chain D against D, TM-score 1.00
Q2CEE3 · AlphaFold monomer V2.0 prediction for protein O-glcnacase (Q2CEE3) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q2CEE3
Elsewhere: RCSB PDB 7KHS · PDBe 7KHS · UniProt Q2CEE3

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