2JKH | pdb_00002jkh

Factor Xa - cation inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb2JKH/pdb

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

Deposited: 2008-08-28 Released: 2009-01-13
Deposition Author(s): Salonen, L.M., Bucher, C., Banner, D.W., Benz, J., Haap, W., Mary, J.L., Schweizer, W.B., Seiler, P., Kuster, O., Diederich, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.221 (Depositor), 0.227 (DCC)
R-Value Work:
0.195 (Depositor), 0.202 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Cation-Pi Interactions at the Active Site of Factor Xa: Dramatic Enhancement Upon Stepwise N-Alkylation of Ammonium Ions.

Salonen, L.M., Bucher, C., Banner, D.W., Haap, W., Mary, J.L., Benz, J., Kuster, O., Seiler, P., Schweizer, W.B., Diederich, F.

(2009) Angew Chem Int Ed Engl 48: 811

PubMed: 19101972 Search on PubMed
DOI: https://doi.org/10.1002/anie.200804695
Primary Citation Related Structures:
2JKH

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 33.76 kDa
Atom Count: 2,792
Modeled Residue Count: 288
Deposited Residue Count: 296
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED FACTOR XA HEAVY CHAIN	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR X LIGHT CHAIN	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BI7 Query on BI7 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3-[(3~{a}~{S},4~{R},8~{a}~{S},8~{b}~{R})-4-[5-(5-chloranylthiophen-2-yl)-1,2-oxazol-3-yl]-1,3-bis(oxidanylidene)-4,6,7,8,8~{a},8~{b}-hexahydro-3~{a}~{H}-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium C₂₂ H₂₈ Cl N₄ O₃ S IMQAZTOPHVBANA-DSYPUSFNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.221 (Depositor), 0.227 (DCC)
R-Value Work: 0.195 (Depositor), 0.202 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.91	α = 90
b = 74.12	β = 90
c = 77.18	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-01-13
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2019-10-30
Changes: Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.2: 2024-11-06
Changes: Structure summary