1A0H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • Also Cited By: 3E6P

  • 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 majo ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MEIZOTHROMBIN
A, D
159Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Go to Gene View: F2
Go to UniProtKB:  P00735
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MEIZOTHROMBIN
B, E
259Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Go to Gene View: F2
Go to UniProtKB:  P00735
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G6
Query on 0G6

Download SDF File 
Download CCD File 
B, E
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
PPACK
C21 H34 Cl N6 O3
DVFLYEYCMMLBTQ-VSZNYVQBSA-O
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020
B,ED-Phe-Pro-Arg-CH2ClPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 186.150α = 90.00
b = 186.150β = 90.00
c = 120.290γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
SCALEKdata reduction
XENGENdata collection
SCALEKdata scaling
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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