1RFN

HUMAN COAGULATION FACTOR IXA IN COMPLEX WITH P-AMINO BENZAMIDINE

• PDB DOI:  https://doi.org/10.2210/pdb1RFN/pdb

• Classification: COAGULATION FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-04-19 Released: 1999-09-01 
• Deposition Author(s): Hopfner, K.-P., Lang, A., Karcher, A., Sichler, K., Kopetzki, E., Brandstetter, H., Huber, R., Bode, W., Engh, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.273 
• R-Value Work: 0.216 

Literature

Coagulation factor IXa: the relaxed conformation of Tyr99 blocks substrate binding.

Hopfner, K.P., Lang, A., Karcher, A., Sichler, K., Kopetzki, E., Brandstetter, H., Huber, R., Bode, W., Engh, R.A.

(1999) Structure 7: 989-996

• PubMed: 10467148 
• DOI: https://doi.org/10.1016/s0969-2126(99)80125-7
• Primary Citation of Related Structures:  
  1RFN


• PubMed Abstract: 
  

  Among the S1 family of serine proteinases, the blood coagulation factor IXa (fIXa) is uniquely inefficient against synthetic peptide substrates. Mutagenesis studies show that a loop of residues at the S2-S4 substrate-binding cleft (the 99-loop) contributes to the low efficiency. The crystal structure of porcine fIXa in complex with the inhibitor D-Phe-Pro-Arg-chloromethylketone (PPACK) was unable to directly clarify the role of the 99-loop, as the doubly covalent inhibitor induced an active conformation of fIXa.

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Organizational Affiliation: 

Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, Martinsried, Germany.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 32.7 kDa 
• Atom Count: 2,306 
• Modelled Residue Count: 292 
• Deposited Residue Count: 292 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COAGULATION FACTOR IX)	A	235	Homo sapiens	Mutation(s): 0  Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
PHAROS:  P00740

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COAGULATION FACTOR IX)	B	57	Homo sapiens	Mutation(s): 0  Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
PHAROS:  P00740

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PBZ	D [auth A]	P-AMINO BENZAMIDINE C7 H10 N3 WPANETAWYGDRLL-UHFFFAOYSA-O
TBU	E [auth A]	TERTIARY-BUTYL ALCOHOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.273 
• R-Value Work: 0.216 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.9	α = 90
b = 90.9	β = 90
c = 151.6	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-09-01 
Deposition Author(s): Hopfner, K.-P., Lang, A., Karcher, A., Sichler, K., Kopetzki, E., Brandstetter, H., Huber, R., Bode, W., Engh, R.A.

Revision History  

• Version 1.0: 1999-09-01
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance