Research workbench

Cpoga D298N in complex with P53-derived O-glcnac peptide

Analyse Cpoga D298N in complex with P53-derived O-glcnac peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YDR
Type: protein
Length: 587 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase nagj; Cellular tumor antigen P53
EC: 3.2.1.52
UniProt: Q0TR53, P04637
Ligands: NAG, CD
Pockets: 7 · best druggability 0.41

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glcnacase nagj (EC 3.2.1.52)	protein	579	47% helix, 16% strand	Q0TR53
P	Cellular tumor antigen P53	protein	8	0% helix, 0% strand	P04637

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, P
CD · Cadmium ion · metal · 18 copies · chains A

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

Pockets

7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.41	0.80	19	CD
2	133	0.41	0.74	15	empty
3	78	0.41	0.78	18	empty
4	93	0.39	0.77	16	empty
5	85	0.37	0.76	15	empty

Interfaces

1 interface between chains.

A–P · 369 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 glycan (O-glycosylation).

Compared structures

2YDR · CpOGA D298N in complex with p53-derived O-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
Every structure of UniProt P04637
Elsewhere: RCSB PDB 2YDR · PDBe 2YDR · UniProt Q0TR53 · UniProt P04637

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