Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 39410.80 
• Atom Count: 2300 
• Residue Count: 350 
• Unique protein chains: 2

1FAX

COAGULATION FACTOR XA INHIBITOR COMPLEX

• DOI: 10.2210/pdb1FAX/pdb

• Classification: COAGULATION FACTOR
• Organism(s): Homo sapiens


• Deposited: 1996-08-23 Released: 1997-10-29 
• Deposition Author(s): Brandstetter, H., Engh, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.261 
• R-Value Work: 0.197 

Literature

X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition.

Brandstetter, H., Kuhne, A., Bode, W., Huber, R., von der Saal, W., Wirthensohn, K., Engh, R.A.

(1996) J.Biol.Chem. 271: 29988-29992

• PubMed: 8939944 
• DOI: 10.1074/jbc.271.47.29988
• Also Cited By: 1WU1, 1V3X, 1QBO, 1QB9


• PubMed Abstract: 
  

The 3.0-A resolution x-ray structure of human des-Gla-coagulation factor Xa (fXa) has been determined in complex with the synthetic inhibitor DX-9065a. The binding geometry is characterized primarily by two interaction sites: the naphthamidine group is fixed in the S1 pocket by a typical salt bridge to Asp-189, while the pyrrolidine ring binds in the unique aryl-binding site (S4) of fXa. Unlike the large majority of inhibitor complexes with serine proteinases, Gly-216 (S3) does not contribute to hydrogen bond formation. In contrast to typical thrombin binding modes, the S2 site of fXa cannot be used by DX-9065a since it is blocked by Tyr-99, and the aryl-binding site (S4) of fXa is lined by carbonyl oxygen atoms that can accommodate positive charges. This has implications for natural substrate recognition as well as for drug design.

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Related Citations: 

• A Novel Factor Xa Inhibitor: Structure-Activity Relationships and Selectivity between Factor Xa and Thrombin
  Katakura, S.,Nagahara, T.,Hara, T.,Iwamoto, M.
  (1993) Biochem.Biophys.Res.Commun. 197: 965
• Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution
  Padmanabhan, K.,Padmanabhan, K.P.,Tulinsky, A.,Park, C.H.,Bode, W.,Huber, R.,Blankenship, D.T.,Cardin, A.D.,Kisiel, W.
  (1993) J.Mol.Biol. 232: 947
• X-Ray Structure of Clotting Factor Ixa: Active Site and Module Structure Related to Xase Activity and Hemophilia B
  Brandstetter, H.,Bauer, M.,Huber, R.,Lollar, P.,Bode, W.
  (1995) Proc.Natl.Acad.Sci.USA 92: 9796




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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Strukturforschung, D-82125 Martinsried, Federal Republic of Germany. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
FACTOR XA	A	254	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Go to Gene View: F10 Go to UniProtKB:  P00742

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
FACTOR XA	L	96	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Go to Gene View: F10 Go to UniProtKB:  P00742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
DX9	A	(2S)-3-(7-carbamimidoylnaphthalen-2-yl)-2-[4-({(3R)-1-[(1Z)-ethanimidoyl]pyrrolidin-3-yl}oxy)phenyl]propanoic acid DX9056A C26 H28 N4 O3 AGRCGQSFFMCBRE-DGUCVARSSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DX9	Ki: 20 - 41 nM (98) BINDINGDB
DX9	IC50: 40 - 130 nM (98) BINDINGDB
DX9	Ki: 41 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.261 
• R-Value Work: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.930	α = 90.00
b = 73.170	β = 90.00
c = 79.080	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
SAINT	data scaling
SAINT	data reduction
X-PLOR	model building
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-08-23 
• Released Date: 1997-10-29 
• Deposition Author(s): Brandstetter, H., Engh, R.A.

Revision History 

• Version 1.0: 1997-10-29
  Type: Initial release
• Version 1.1: 2008-03-10
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance