5CM4
Crystal structure of human Frizzled 4 Cysteine-Rich Domain (CRD)
- PDB DOI: https://doi.org/10.2210/pdb5CM4/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2015-07-16 Released: 2015-08-12 
- Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.255 
- R-Value Work: 0.226 
- R-Value Observed: 0.227 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Frizzled-4 | 125 | Homo sapiens | Mutation(s): 0  Gene Names: FZD4 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9ULV1 (Homo sapiens) Explore Q9ULV1  Go to UniProtKB:  Q9ULV1 | |||||
PHAROS:  Q9ULV1 GTEx:  ENSG00000174804  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9ULV1 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | D [auth A], E [auth B], F [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.255 
- R-Value Work: 0.226 
- R-Value Observed: 0.227 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 105.583 | α = 90 |
b = 111.738 | β = 90 |
c = 75.37 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-08-12  Deposition Author(s): Ke, J., Parker, N., Gu, X., Zhang, C., Melcher, K., Xu, H.E.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) | United States | DK071662 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM102545 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM104212 |
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor | United States | 085P1000817 |
Revision History (Full details and data files)
- Version 1.0: 2015-08-12
Type: Initial release - Version 1.1: 2015-09-16
Changes: Database references - Version 1.2: 2017-09-27
Changes: Author supporting evidence, Derived calculations - Version 1.3: 2019-12-25
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary