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.

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

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
784 Query on 784 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	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		Interactions Focus chain C [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A]

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-06-16

Deposition Author(s):

Revision History (Full details and data files)

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