Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.01 kDa 
• Atom Count: 2552 
• Modelled Residue Count: 286 
• Deposited Residue Count: 293 
• Unique protein chains: 2

5JBB

Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with EGR-chloromethylketone

• DOI: 10.2210/pdb5JBB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-04-13 Released: 2016-06-01 
• Deposition Author(s): Kristensen, L.H., Brandstetter, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.190 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site.

Kristensen, L.H., Olsen, O.H., Blouse, G.E., Brandstetter, H.

(2016) Biochem J 473: 2395-2411

• PubMed: 27208168 
• DOI: 10.1042/BCJ20160336
• Primary Citation of Related Structures:  
  5JBB, 5JBA, 5JBC, 5JB8, 5JB9


• PubMed Abstract: 
  

Coagulation Factor IX is positioned at the merging point of the intrinsic and extrinsic blood coagulation cascades. Factor IXa (activated Factor IX) serves as the trigger for amplification of coagulation through formation of the so-called Xase complex, which is a ternary complex of Factor IXa, its substrate Factor X and the cofactor Factor VIIIa on the surface of activated platelets. Within the Xase complex the substrate turnover by Factor IXa is enhanced 200000-fold; however, the mechanistic and structural basis for this dramatic enhancement remains only partly understood. A multifaceted approach using enzymatic, biophysical and crystallographic methods to evaluate a key set of activity-enhanced Factor IXa variants has demonstrated a delicately balanced bidirectional network. Essential molecular interactions across multiple regions of the Factor IXa molecule co-operate in the maturation of the active site. This maturation is specifically facilitated by long-range communication through the Ile(212)-Ile(213) motif unique to Factor IXa and a flexibility of the 170-loop that is further dependent on the conformation in the Cys(168)-Cys(182) disulfide bond. Ultimately, the network consists of compensatory brakes (Val(16) and Ile(213)) and accelerators (Tyr(99) and Phe(174)) that together allow for a subtle fine-tuning of enzymatic activity.

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Organizational Affiliation: 

Structural Biology Group, Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	A [auth E]	58	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 GTEx:  ENSG00000101981

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B [auth S]	235	Homo sapiens	Mutation(s): 4  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 GTEx:  ENSG00000101981

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0GJ	D [auth S]	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide C14 H28 Cl N6 O5 XELWNHKFCNMWQO-LPEHRKFASA-O
DMS	E [auth S]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	C [auth S]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000288 (0GJ)	D [auth S]	GLU-GLY-ARG-CHLOROMETHYL KETONE	Peptide-like /  Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.190 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.31	α = 90
b = 66.61	β = 90
c = 97.05	γ = 90

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-04-13 
• Released Date: 2016-06-01 
Deposition Author(s): Kristensen, L.H., Brandstetter, H.

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Non-polymer description
• Version 1.2: 2018-01-24
  Changes: Source and taxonomy