1ABI

STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the hirulog 3-thrombin complex and nature of the S' subsites of substrates and inhibitors.

Qiu, X.Padmanabhan, K.P.Carperos, V.E.Tulinsky, A.Kline, T.Maraganore, J.M.Fenton 2nd., J.W.

(1992) Biochemistry 31: 11689-11697

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray crystallographic structure of the human alpha-thrombin complex with hirulog 3 (a potent, noncleavable hirudin-based peptide of the "hirulog" class containing a beta-homoarginine at the scissile bond), which is isomorphous with that of the h ...

    The X-ray crystallographic structure of the human alpha-thrombin complex with hirulog 3 (a potent, noncleavable hirudin-based peptide of the "hirulog" class containing a beta-homoarginine at the scissile bond), which is isomorphous with that of the hirugen-thrombin crystal structure, was solved at 2.3-A resolution by starting with a model for thrombin derived from the hirugen-thrombin complex and was refined by restrained least squares methods (R = 0.132). Residues of hirulog 3 were well-defined in the electron density, which included most of the pentaglycine linker and the C-terminal helical turn that was disordered in a related structure of thrombin with hirulog 1. The interactions of D-Phe1'-Pro2'-beta-homoArg3' with the active site of thrombin were essentially identical to those of related structures of PPACK- (D-Phe-Pro-Arg chloromethyl ketone) and hirulog 1-thrombin, with the guanidinium function of the arginyl P1 residue forming a hydrogen-bonding ion pair with Asp189 of the S1 site. A noticeable shift in the CA atom of beta-homoArg3' due to the methylene insertion displaces the scissile bond from attack by Ser195, thus imparting proteolytic stability to the beta-homoArg hirulog derivative. Resolution of the pentaglycine spacer, linking N- and C-terminal functional domains into a single oligopeptide bivalent inhibitor, permitted delineation of corresponding S' subsites of thrombin. The position of Gly4' (P1') is stabilized by three hydrogen bonds with His57, Lys60F, and Ser195, while the conformational angles maintained in a strained, nonallowed configuration for non-glycyl amino acids.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • 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
    • Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin
      Skrzypczak-Jankun, E.,Carperos, V.,Ravichandran, K.G.,Tulinsky, A.,Westbrook, M.,Maraganore, J.M.
      (1991) J.Mol.Biol. 221: 1379
    • 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
      Bode, W.,Mayr, I.,Baumann, U.,Huber, R.,Stone, S.R.,Hofsteenge, J.
      (1989) Embo J. 8: 3467


    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing 48824-1322.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (SMALL SUBUNIT)
L
36Homo sapiensMutation(s): 0 
Gene 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 sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIRULOG 3
I
20Hirudo medicinalisMutation(s): 0 
Find proteins for P28504 (Hirudo medicinalis)
Go to UniProtKB:  P28504
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HMR
Query on HMR
I
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
DPN
Query on DPN
I
D-PEPTIDE LINKINGC9 H11 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.440α = 90.00
b = 72.100β = 101.02
c = 73.070γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1992-08-24 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Qiu, X., Tulinsky, A.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    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