2YGP

WIF domain-EGF-like domain 1 Met77Trp of human Wnt inhibitory factor 1 in complex with 1,2-dipalmitoylphosphatidylcholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 2YGP

Classification: SIGNALING PROTEIN

Total Structure Weight: 22271.65

Macromolecule Entities
Molecule Chains Length Organism Details
WNT INHIBITORY FACTOR 1 A 188 Homo sapiens Fragment: WIF DOMAIN-EGF-LIKE DOMAIN 1, RESIDUES 35-210
Mutation: M77W, Q166X
Gene Name(s): WIF1 Gene View UNQ191/PRO217
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PCF
Query on PCF

A 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SPD
Query on SPD

A SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) (Synonym)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MLY
Query on MLY
A L-PEPTIDE LINKING C8 H18 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.185
  • Space Group: C 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 50.76 α = 90.00
b = 134.24 β = 90.00
c = 60.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-19
  • Released Date: 2011-07-13
  • Deposition author(s): Malinauskas, T., Aricescu, A.R., Lu, W., Siebold, C., Jones, E.Y.

Revision History

  • 2011-08-17
    Type: Database references