1A0H

THE X-RAY CRYSTAL STRUCTURE OF PPACK-MEIZOTHROMBIN DESF1: KRINGLE/THROMBIN AND CARBOHYDRATE/KRINGLE/THROMBIN INTERACTIONS AND LOCATION OF THE LINKER CHAIN

• PDB DOI:  https://doi.org/10.2210/pdb1A0H/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1997-11-30 Released: 1998-06-17 
• Deposition Author(s): Martin, P.D., Malkowski, M.G., Box, J., Esmon, C.T., Edwards, B.F.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK.

Martin, P.D., Malkowski, M.G., Box, J., Esmon, C.T., Edwards, B.F.

(1997) Structure 5: 1681-1693

• PubMed: 9438869 
• DOI: https://doi.org/10.1016/s0969-2126(97)00314-6
• Primary Citation of Related Structures:  
  1A0H


• PubMed Abstract: 
  

  The conversion of prothrombin to thrombin by factor Xa is the penultimate step in the blood clotting cascade. In vivo, where the conversion occurs primarily on activated platelets in association with factor Va and Ca2+ ions, meizothrombin is the major intermediate of the two step reaction. Meizothrombin rapidly loses the fragment 1 domain (F1) by autolysis to become meizothrombin des F1 (mzTBN-F1). The physiological properties of mzTBN-F1 differ dramatically from those of thrombin due to the presence of prothrombin fragment 2 (F2), which remains covalently attached to the activated thrombin domain in mzTBN-F1.

---

Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 97.04 kDa 
• Atom Count: 6,901 
• Modelled Residue Count: 836 
• Deposited Residue Count: 836 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEIZOTHROMBIN	A, C [auth D]	159	Bos taurus	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt
Find proteins for P00735 (Bos taurus) Explore P00735  Go to UniProtKB:  P00735

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MEIZOTHROMBIN	B, D [auth E]	259	Bos taurus	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt
Find proteins for P00735 (Bos taurus) Explore P00735  Go to UniProtKB:  P00735

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0G6	G [auth B], H [auth E]	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide C21 H34 Cl N6 O3 DVFLYEYCMMLBTQ-VSZNYVQBSA-O

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6)	G [auth B], H [auth E]	D-Phe-Pro-Arg-CH2Cl	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.15	α = 90
b = 186.15	β = 90
c = 120.29	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
SCALEK	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
SCALEK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-17 
Deposition Author(s): Martin, P.D., Malkowski, M.G., Box, J., Esmon, C.T., Edwards, B.F.P.

Revision History  

• Version 1.0: 1998-06-17
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2013-02-27
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary