2BOK

Factor Xa - cation

• PDB DOI: https://doi.org/10.2210/pdb2BOK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-04-12 Released: 2005-06-16 
• Deposition Author(s): Morgenthaler, M., Schaerer, K., Paulini, R., Obst-Sander, U., Banner, D.W., Schlatter, D., Benz, J., Stihle, M., Diederich, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.237 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Quantification of Cation-Pi Interactions in Protein-Ligand Complexes: Crystal-Structure Analysis of Factor Xa Bound to a Quaternary Ammonium Ion Ligand

Scharer, K., Morgenthaler, M., Paulini, R., Obst-Sander, U., Banner, D.W., Schlatter, D., Benz, J., Stihle, M., Diederich, F.

(2005) Angew Chem Int Ed Engl 44: 4400

• PubMed: 15952226 
• DOI: https://doi.org/10.1002/anie.200500883
• Primary Citation of Related Structures:  
  2BOK

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Organizational Affiliation: 

Laboratorium für Organische Chemie, ETH Hönggerberg, HCI, 8093 Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 33.66 kDa 
• Atom Count: 2,421 
• Modelled Residue Count: 273 
• Deposited Residue Count: 296 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X	A	241	Homo sapiens	Mutation(s): 1  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X	B [auth L]	55	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
784	C [auth A]	[AMINO (4-{(3AS,4R,8AS,8BR)-1,3-DIOXO-2- [3-(TRIMETHYLAMMONIO) PROPYL]DECAHYDROPYRROLO[3,4-A] PYRROLIZIN-4-YL}PHENYL) METHYLENE]AMMONIUM C22 H32 N5 O2 JCLUABDCGDTVPA-VJANTYMQSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
784	PDBBind:  2BOK	Ki: 280 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.237 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.84	α = 90
b = 71.67	β = 90
c = 72.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-16 
Deposition Author(s): Morgenthaler, M., Schaerer, K., Paulini, R., Obst-Sander, U., Banner, D.W., Schlatter, D., Benz, J., Stihle, M., Diederich, F.

Revision History  

• Version 1.0: 2005-06-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary