6AHY

Wnt signaling complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Frizzled-8
A, C, E
141Mus musculusMutation(s): 0 
Gene Names: Fzd8
UniProt & NIH Common Fund Data Resources
Find proteins for Q61091 (Mus musculus)
Explore Q61091 
Go to UniProtKB:  Q61091
IMPC:  MGI:108460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61091
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene Wnt-3
B, D, F
319Homo sapiensMutation(s): 0 
Gene Names: WNT3INT4
UniProt & NIH Common Fund Data Resources
Find proteins for P56703 (Homo sapiens)
Explore P56703 
Go to UniProtKB:  P56703
PHAROS:  P56703
GTEx:  ENSG00000108379 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56703
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAM
Query on PAM

Download Ideal Coordinates CCD File 
L [auth B],
O [auth D]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
N [auth D]
P [auth E]
I [auth A],
K [auth B],
M [auth C],
N [auth D],
P [auth E],
Q [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, C, E
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.073α = 90
b = 141.611β = 90
c = 260.692γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary