MolNFT v1 · #85857 · protein

Crystal structure of human POFUT2

4AP5 · GDP-fucose protein O-fucosyltransferase 2: “Crystal structure of human POFUT2”. X-ray diffraction, 3 ligands (NAG, MG, CL), 6 pockets (best druggability 0.81). MolNFT v1 #85857 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4AP5
Type: protein
Length: 778 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GDP-fucose protein O-fucosyltransferase 2
EC: 2.4.1.221
UniProt: Q9Y2G5
Ligands: NAG, MG, CL
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GDP-fucose protein O-fucosyltransferase 2 (EC 2.4.1.221)	protein	389	36% helix, 19% strand	Q9Y2G5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
MG · Magnesium ion · metal · chains B
CL · Chloride ion · ion · 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	1031	0.81	0.82	75	CL
2	1178	0.80	0.81	107	empty
3	411	0.75	0.85	61	empty
4	70	0.63	0.91	23	empty
5	114	0.42	0.76	24	empty

Interfaces

1 interface between chains.

A–B · 1826 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4AP5 · Crystal structure of human POFUT2 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y2G5 · AlphaFold monomer V2.0 prediction for GDP-fucose protein O-fucosyltransferase 2 (Q9Y2G5) · a predicted model of the same protein · chain A 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 Q9Y2G5
Elsewhere: RCSB PDB 4AP5 · PDBe 4AP5 · UniProt Q9Y2G5

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