Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 84.99 kDa 
• Atom Count: 6669 
• Residue Count: 708 
• Unique protein chains: 3

3KCG

Crystal structure of the antithrombin-factor IXa-pentasaccharide complex

• DOI: 10.2210/pdb3KCG/pdb

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


• Deposited: 2009-10-21 Released: 2010-02-02 
• Deposition Author(s): Huntington, J.A., Johnson, D.J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.230 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-A structure of the ternary complex.

Johnson, D.J., Langdown, J., Huntington, J.A.

(2010) Proc Natl Acad Sci U S A 107: 645-650

• PubMed: 20080729 
• DOI: 10.1073/pnas.0910144107
• Primary Citation of Related Structures:  
  3KCG


• PubMed Abstract: 
  

Factor (f) IXa is a critical enzyme for the formation of stable blood clots, and its deficiency results in hemophilia. The enzyme functions at the confluence of the intrinsic and extrinsic pathways by binding to fVIIIa and rapidly generating fXa. In spite of its importance, little is known about how fIXa recognizes its cofactor, its substrate, or its only known inhibitor, antithrombin (AT). However, it is clear that fIXa requires extensive exosite interactions to present substrates for efficient cleavage. Here we describe the 1.7-A crystal structure of fIXa in its recognition (Michaelis) complex with heparin-activated AT. It represents the highest resolution structure of both proteins and allows us to address several outstanding issues. The structure reveals why the heparin-induced conformational change in AT is required to permit simultaneous active-site and exosite interactions with fIXa and the nature of these interactions. The reactive center loop of AT has evolved to specifically inhibit fIXa, with a P2 Gly so as not to clash with Tyr99 on fIXa, a P4 Ile to fit snugly into the S4 pocket, and a C-terminal extension to exploit a unique wall-like feature of the active-site cleft. Arg150 is at the center of the exosite interface, interacting with AT residues on beta-sheet C. A surprising crystal contact is observed between the heparin pentasaccharide and fIXa, revealing a plausible mode of binding that would allow longer heparin chains to bridge the complex.

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Organizational Affiliation: 

Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IXa light chain	L	59	Homo sapiens	Mutation(s): 0  Gene Names: F9 EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
NIH Common Fund Data Resources
PHAROS  P00740 GTEx  ENSG00000101981

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IXa heavy chain	H	235	Homo sapiens	Mutation(s): 1  Gene Names: F9 EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
NIH Common Fund Data Resources
PHAROS  P00740 GTEx  ENSG00000101981

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	I	432	Homo sapiens	Mutation(s): 1  Gene Names: SERPINC1, AT3, PRO0309
Find proteins for P01008 (Homo sapiens) Explore P01008  Go to UniProtKB:  P01008
NIH Common Fund Data Resources
PHAROS  P01008 GTEx  ENSG00000117601

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	A, C	2		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside	D	5		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	I	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	H	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900031	D	heparin pentasaccharide	Oligosaccharide /  Anticoagulant		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.230 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.78	α = 90
b = 88.44	β = 90
c = 147.23	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-21 
• Released Date: 2010-02-02 
Deposition Author(s): Huntington, J.A., Johnson, D.J.D.

Revision History 

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary