4F0A

Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8

Structural Biology Knowledgebase: 4F0A SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 4F0A

Classification: SIGNALING PROTEIN

Total Structure Weight: 52603.88

Macromolecule Entities
Molecule Chains Length Organism Details
Frizzled-8 A 132 Mus musculus Fragment: cysteine-rich domain, UNP residues 28-150
Gene Name(s): Fzd8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Protein Wnt-8 B 316 Xenopus laevis Fragment: UNP residues 23-338
Gene Name(s): wnt8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PAM
Query on PAM

B PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.204
  • Space Group: P 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.07 α = 90.00
b = 110.07 β = 90.00
c = 82.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-03
  • Released Date: 2012-06-13
  • Deposition author(s): Janda, C.Y., Waghray, D., Levin, A.M., Thomas, C., Garcia, K.C.

Revision History

  • 2013-10-09
    Type: Non-polymer description | Details: --
  • 2013-09-25
    Type: Binding sites and description | Details: --
  • 2013-09-25
    Type: Biological assembly | Details: --
  • 2013-09-25
    Type: Non-polymer description | Details: --
  • 2012-07-18
    Type: Citation | Details: Citation update