Research workbench

Cpoga D298N in complex with hoga-derived S-glcnac peptide

Analyse Cpoga D298N in complex with hoga-derived S-glcnac peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RHE
Type: protein
Length: 585 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase nagj; Acy-ala-his-cys-gly-NH2
EC: 3.2.1.169
UniProt: Q0TR53
Ligands: NAG, CD, NH2
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glcnacase nagj (EC 3.2.1.169)	protein	581	46% helix, 15% strand	Q0TR53
D	Acy-ala-his-cys-gly-NH2	protein	4	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, D
CD · Cadmium ion · metal · 25 copies · chains A, D
NH2 · Amino group · ion · chains A, D
ACY · Acetic acid · additive · chains A, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.70	0.98	20	NAG
2	80	0.45	0.81	19	empty
3	166	0.44	0.74	19	CD
4	82	0.35	0.75	16	empty
5	73	0.35	0.76	19	empty

Interfaces

1 interface between chains.

A–D · 252 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 glycan (additive adduct, glycosylation).

Compared structures

6RHE · CpOGA D298N in complex with hOGA-derived S-GlcNAc peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q0TR53 · AlphaFold monomer V2.0 prediction for O-glcnacase nagj (Q0TR53) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q0TR53
Elsewhere: RCSB PDB 6RHE · PDBe 6RHE · UniProt Q0TR53

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