Research workbench

Xcogt in complex with udp-S-glcnac

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

PDB: 2XGO
Type: protein
Length: 1,089 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xcogt
UniProt: Q8PC69
Ligands: ZKD
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xcogt	protein	548	51% helix, 11% strand	Q8PC69
B	Xcogt	protein	541	50% helix, 10% strand	Q8PC69

Ligands and binding sites

ZKD · Uridine-diphosphate-1-deoxy-1-thio-N-acetylglucosamine · ligand · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	688	0.75	0.81	96	empty
2	663	0.73	0.80	76	ZKD
3	316	0.61	0.78	39	empty
4	384	0.58	0.76	40	empty
5	165	0.49	0.77	34	empty

Interfaces

1 interface between chains.

A–B · 750 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2XGO · XcOGT in complex with UDP-S-GlcNAc · 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 Q8PC69
Elsewhere: RCSB PDB 2XGO · PDBe 2XGO · UniProt Q8PC69

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