4XE4

Coagulation Factor XII protease domain crystal structure

• PDB DOI: https://doi.org/10.2210/pdb4XE4/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2014-12-22 Released: 2015-02-04 
• Deposition Author(s): Pathak, M., Wilmann, P., Awford, J., Li, C., Fisher, P.M., Dreveny, I., Dekker, L.V., Emsley, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.295 
• R-Value Work: 0.218 
• R-Value Observed: 0.222 

Literature

Coagulation factor XII protease domain crystal structure.

Pathak, M., Wilmann, P., Awford, J., Li, C., Hamad, B.K., Fischer, P.M., Dreveny, I., Dekker, L.V., Emsley, J.

(2015) J Thromb Haemost 13: 580-591

• PubMed: 25604127 
• DOI: https://doi.org/10.1111/jth.12849
• Primary Citation of Related Structures:  
  4XDE, 4XE4


• PubMed Abstract: 
  

  Coagulation factor XII is a serine protease that is important for kinin generation and blood coagulation, cleaving the substrates plasma kallikrein and FXI.

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Organizational Affiliation: 

Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, UK.

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: 28.35 kDa 
• Atom Count: 1,894 
• Modelled Residue Count: 231 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XII	A	255	Homo sapiens	Mutation(s): 1  Gene Names: F12 EC: 3.4.21.38
UniProt & NIH Common Fund Data Resources
Find proteins for P00748 (Homo sapiens) Explore P00748  Go to UniProtKB:  P00748
PHAROS:  P00748 GTEx:  ENSG00000131187

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

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_900017	B	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.295 
• R-Value Work: 0.218 
• R-Value Observed: 0.222 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.06	α = 90
b = 137.06	β = 90
c = 37.011	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-02-04 
Deposition Author(s): Pathak, M., Wilmann, P., Awford, J., Li, C., Fisher, P.M., Dreveny, I., Dekker, L.V., Emsley, J.

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Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references
• Version 1.2: 2015-10-28
  Changes: 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: 2024-01-10
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary