Research workbench

Crystal structure of human gnt-V luminal domain in apo form

Analyse Crystal structure of human gnt-V luminal domain in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZIB
Type: protein
Length: 579 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-1,6-mannosylglycoprotein 6-beta-N- acetylglucosaminyltransferase a
EC: 2.4.1.155
UniProt: Q09328
Ligands: NAG
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-1,6-mannosylglycoprotein 6-beta-N- acetylglucosaminyltransferase a (EC 2.4.1.155)	protein	579	39% helix, 15% strand	Q09328

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A

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

Pockets

6 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	60	0.72	0.98	25	empty
2	629	0.69	0.77	65	empty
3	275	0.63	0.80	45	empty
4	313	0.61	0.79	33	empty
5	118	0.39	0.75	23	empty

Modifications

Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5ZIB · Crystal structure of human GnT-V luminal domain in apo form · the same entry in another collection · chain A against A, TM-score 1.00
Q09328 · AlphaFold monomer V2.0 prediction for alpha-1,6-mannosylglycoprotein… · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q09328
Elsewhere: RCSB PDB 5ZIB · PDBe 5ZIB · UniProt Q09328

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.