2JKH

Factor Xa - cation inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report



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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACTIVATED FACTOR XA HEAVY CHAIN
A
241Homo sapiensMutation(s): 1 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FACTOR X LIGHT CHAIN
L
55Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BI7
Query on BI7

Download CCD File 
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
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BI7Ki:  9   nM  Binding MOAD
BI7Ki :  9   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.91α = 90
b = 74.12β = 90
c = 77.18γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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