4DG6 | pdb_00004dg6

Crystal structure of domains 1 and 2 of LRP6

• PDB DOI: https://doi.org/10.2210/pdb4DG6/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2012-01-25 Released: 2012-06-13 
• Deposition Author(s): Ceska, T.A., Doyle, C., Slocombe, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.313 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Characterization of the interaction of sclerostin with the LRP family of Wnt co-receptors

Holdsworth, G., Slocombe, P., Doyle, C., Sweeney, B., Veverka, V., Le Rich, K., Franklin, R.J., Brookings, D., Turner, J., Kennedy, J., Garlish, R., Shi, J., Newnham, L., McMillan, D., Muzylak, M., Carr, M., Henry, A.J., Ceska, T., Robinson, M.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.07 kDa 
• Atom Count: 5,005 
• Modeled Residue Count: 616 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 6	A	616	Homo sapiens	Mutation(s): 0  Gene Names: LRP6
UniProt & NIH Common Fund Data Resources
Find proteins for O75581 (Homo sapiens) Explore O75581  Go to UniProtKB:  O75581
PHAROS:  O75581 GTEx:  ENSG00000070018
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: O75581-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.313 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.36	α = 90
b = 109.36	β = 90
c = 130.88	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Ceska, T.A., Doyle, C., Slocombe, P.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary