1PPB

THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.

Bode, W.Mayr, I.Baumann, U.Huber, R.Stone, S.R.Hofsteenge, J.

(1989) EMBO J. 8: 3467-3475

  • Also Cited By: 1DWB, 1DWC, 1DWD, 1DWE

  • PubMed Abstract: 
  • A stoichiometric complex formed between human alpha-thrombin and D-Phe-Pro-Arg chloromethylketone was crystallized in an orthorhombic crystal form. Orientation and position of a starting model derived from homologous modelling were determined by Patt ...

    A stoichiometric complex formed between human alpha-thrombin and D-Phe-Pro-Arg chloromethylketone was crystallized in an orthorhombic crystal form. Orientation and position of a starting model derived from homologous modelling were determined by Patterson search methods. The thrombin model was completed in a cyclic modelling-crystallographic refinement procedure to a final R-value of 0.171 for X-ray data to 1.92 A. The structure is in full agreement with published cDNA sequence data. The A-chain, ordered only in its central part, is positioned along the molecular surface opposite to the active site. The B-chain exhibits the characteristic polypeptide fold of trypsin-like proteinases. Several extended insertions form, however, large protuberances; most important for interaction with macromolecular substrates is the characteristic thrombin loop around Tyr60A-Pro60B-Pro60C-Trp60D (chymotrypsinogen numbering) and the enlarged loop around the unique Trp148. The former considerably restricts the active site cleft and seems likely to be responsible for poor binding of most natural proteinase inhibitors to thrombin. The exceptional specificity of D-Phe-Pro-Arg chloromethylketone can be explained by a hydrophobic cage formed by Ile174, Trp215, Leu99, His57, Tyr60A and Trp60D. The narrow active site cleft, with a more polar base and hydrophobic rims, extends towards the arginine-rich surface of loop Lys70-Glu80 that probably represents part of the anionic binding region for hirudin and fibrinogen.


    Related Citations: 
    • Refined Structure of the Hirudin-Thrombin Complex
      Rydel, T.J.,Tulinsky, A.,Bode, W.,Huber, R.
      (1991) J.Mol.Biol. 221: 583
    • Refined 2.3 Angstroms X-Ray Crystal Structure of Bovine Thrombin Complexes Formed with the Benzamidine and Arginine-Based Thrombin Inhibitors Napap, 4-Tapap and Mqpa. A Starting Point for Improving Anti-Thrombotics
      Brandstetter, H.,Turk, D.,Hoeffken, H.W.,Grosse, D.,Stuerzebecher, J.,Martin, P.D.,Edwards, B.F.P.,Bode, W.
      (1992) J.Mol.Biol. 226: 1085
    • Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition
      Gruetter, M.G.,Priestle, J.P.,Rahnel, J.,Grossenbacher, H.,Bode, W.,Hofsteenge, J.,Stone, S.R.
      (1990) Embo J. 9: 2361
    • The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin
      Rydel, T.J.,Ravichandran, K.G.,Tulinsky, A.,Bode, W.,Huber, R.,Roitsch, C.,Fenton II, J.W.
      (1990) Science 249: 277
    • The Spatial Structure of Thrombin as a Guide to its Multiple Sites of Interaction
      Bode, W.,Stubbs, M.
      (1993) Semin.Thromb.Hemostasis 19: 321
    • Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophe
      Bode, W.,Turk, D.,Stuerzebecher, J.
      (1990) Eur.J.Biochem. 193: 175
    • Human D-Phe-Pro-Arg-Ch2-Alpha-Thrombin Crystallization and Diffraction Data
      Skrzypczak-Jankun, E.,Rydel, T.J.,Tulinsky, A.,Fenton II, J.W.,Mann, K.G.
      (1989) J.Mol.Biol. 206: 755
    • The Interaction of Thrombin with Fibrinogen. A Structural Basis for its Specificity
      Stubbs, M.T.,Oschkinat, H.,Mayr, I.,Huber, R.,Angliker, H.,Stone, S.R.,Bode, W.
      (1992) Eur.J.Biochem. 206: 187
    • X-Ray Crystal Structures of Human Alpha-Thrombin and of the Human Thrombin-Hirudin Complex
      Bode, W.,Huber, R.,Rydel, T.J.,Tulinsky, A.
      (1992) Thrombin: Structure and Function --: 3
    • The Refined 1.9-Angstroms Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin. Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Properties
      Bode, W.,Turk, D.,Karshikov, A.
      (1992) Protein Sci. 1: 426
    • The Electrostatic Properties of Thrombin: Importance for Structural Stabilization and Ligand Binding
      Karshikov, A.,Bode, W.
      (1993) Semin.Thromb.Hemostasis 19: 334
    • Electrostatic Interactions in the Association of Proteins: An Analysis of the Thrombin-Hirudin Complex
      Karshikov, A.,Bode, W.,Tulinsky, A.,Stone, S.R.
      (1992) Protein Sci. 1: 727


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, FRG.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (SMALL SUBUNIT)
L
36Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (LARGE SUBUNIT)
H
259Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G6
Query on 0G6

Download SDF File 
Download CCD File 
H
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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020
HD-Phe-Pro-Arg-CH2ClPeptide-like / Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.740α = 90.00
b = 67.810β = 90.00
c = 61.070γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1991-10-24 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Bode, W.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-07
    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: 2013-02-27
    Type: Other