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Wif domain-EGF-like domain 1 of human wnt inhibitory factor 1 in complex with 1,2-dipalmitoylphosphatidylcholine

Analyse Wif domain-EGF-like domain 1 of human wnt inhibitory factor 1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2YGO
Type
protein
Length
180 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Wnt inhibitory factor 1
UniProt
Q9Y5W5
Ligands
PCF, NAG, NA
Pockets
1 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 39% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AWnt inhibitory factor 1protein1809% helix, 39% strandQ9Y5W5

Ligands and binding sites

  • PCF · 1,2-diacyl-sn-glycero-3-phoshocholine · ligand · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
  • NA · Sodium ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15080.820.8843PCF

Modifications

Observed in the structure: 6 modified, 4 disulfide, 1 glycan (methylation, disulfide, N-glycosylation).

Compared structures

  • 2YGO · WIF domain-EGF-like domain 1 of human Wnt inhibitory factor 1 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9Y5W5 · AlphaFold monomer V2.0 prediction for wnt inhibitory factor 1 (Q9Y5W5) · a predicted model of the same protein · chain A against A, TM-score 0.98

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