5URY

Crystal structure of Frizzled 5 CRD in complex with PAM

• PDB DOI: https://doi.org/10.2210/pdb5URY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2017-02-13 Released: 2017-05-10 
• Deposition Author(s): Mukund, S., Nile, A.H., Stanger, K., Hannoush, R.N., Wang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.206 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.71 kDa 
• Atom Count: 2,151 
• Modelled Residue Count: 240 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-5	A, B	146	Homo sapiens	Mutation(s): 0  Gene Names: FZD5, C2orf31
UniProt & NIH Common Fund Data Resources
Find proteins for Q13467 (Homo sapiens) Explore Q13467  Go to UniProtKB:  Q13467
PHAROS:  Q13467 GTEx:  ENSG00000163251

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47513BB GlyCosmos:  G47513BB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAM	D [auth A], E [auth B]	PALMITOLEIC ACID C16 H30 O2 SECPZKHBENQXJG-FPLPWBNLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.206 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.412	α = 90
b = 123.412	β = 90
c = 46.951	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Mukund, S., Nile, A.H., Stanger, K., Hannoush, R.N., Wang, W.

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary