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Mouse POFUT1 in complex with EGF(+) and GDP

Analyse Mouse POFUT1 in complex with EGF(+) and GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KY5
Type: protein
Length: 392 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GDP-fucose protein O-fucosyltransferase 1; EGF(+)
EC: 2.4.1.221
UniProt: Q91ZW2
Ligands: GDP, NAG
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221)	protein	352	42% helix, 16% strand	Q91ZW2
B	EGF(+)	protein	40	10% helix, 25% strand	—

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
GOL · Glycerol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	509	0.74	0.82	47	GDP
2	335	0.62	0.78	50	empty
3	57	0.44	0.83	14	empty

Interfaces

1 interface between chains.

A–B · 903 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5KY5 · mouse POFUT1 in complex with EGF(+) and GDP · the same entry in another collection · chain A against A, TM-score 1.00
Q91ZW2 · AlphaFold monomer V2.0 prediction for GDP-fucose protein O-fucosyltransferase 1 (Q91ZW2) · a predicted model of the same protein · 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 Q91ZW2
Elsewhere: RCSB PDB 5KY5 · PDBe 5KY5 · UniProt Q91ZW2

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