5HZV

Crystal structure of the zona pellucida module of human endoglin/CD105

• PDB DOI: https://doi.org/10.2210/pdb5HZV/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-02-03 Released: 2017-06-07 
• Deposition Author(s): Bokhove, M., Saito, T., Jovine, L.
• Funding Organization(s): Karolinska Institutet, Center for Biosciences, Swedish Research Council, Gustafsson Foundation for Research in Natural Sciences and Medicine, Sven and Ebba-Christina Hagberg foundation, European Molecular Biology Organization, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.272 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.66 kDa 
• Atom Count: 4,626 
• Modelled Residue Count: 598 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Endoglin	A	626	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 13  Gene Names: malE, b4034, JW3994, ENG, END
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P17813 (Homo sapiens) Explore P17813  Go to UniProtKB:  P17813
PHAROS:  P17813 GTEx:  ENSG00000106991
UniProt Groups	P17813P0AEX9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.272 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.16	α = 90
b = 125.16	β = 90
c = 88.54	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Bokhove, M., Saito, T., Jovine, L.

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Funding Organization	Location	Grant Number
Karolinska Institutet	Sweden	--
Center for Biosciences	Sweden	--
Swedish Research Council	Sweden	2012-5093
Gustafsson Foundation for Research in Natural Sciences and Medicine	Sweden	--
Sven and Ebba-Christina Hagberg foundation	Sweden	--
European Molecular Biology Organization		--
European Union		ERC 260759

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-06-14
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary