1HBT

Human alpha-thrombin complexed with a peptidyl pyridinium methyl ketone containing bivalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a peptidyl pyridinium methyl ketone inhibitor with thrombin.

Rehse, P.H.Steinmetzer, T.Li, Y.Konishi, Y.Cygler, M.

(1995) Biochemistry 34: 11537-11544


  • PubMed Abstract: 
  • The crystal structure of a complex between a bivalent peptidyl pyridinium methyl ketone inhibitor and human alpha-thrombin has been solved and refined at 2.0 A to an R factor of 0.18. The inhibitor, (D)cyclohexylalanine-Pro-Arg-(CH2N+C5H4CH2CO)-(Gly) ...

    The crystal structure of a complex between a bivalent peptidyl pyridinium methyl ketone inhibitor and human alpha-thrombin has been solved and refined at 2.0 A to an R factor of 0.18. The inhibitor, (D)cyclohexylalanine-Pro-Arg-(CH2N+C5H4CH2CO)-(Gly)4-Asp- Tyr-Glu-Pro-Ile-Pro-Glu-Glu-Ala-cyclo-hexylalanine-(D)Glu (coded P596), which forms a reversible covalent complex with thrombin, is highly potent with a Ki = 4.6 +/- 1.0 x 10(-14) M, lower than that of recombinant hirudin. The N-terminal, active-site-directed portion of the inhibitor is linked to the fibrinogen recognition exosite binding portion by a tetraglycine segment. The strong electron-withdrawing effect provided by the permanent positive charge on the pyridinium nitrogen makes the arginyl carbonyl carbon more susceptible to nucleophilic attack. In the crystal, a covalent P596-thrombin complex is observed. The electron density surrounding the active site portion and the pyridinium of the inhibitor is very well defined, clearly showing the existence of a covalent bond between the Ser195 O gamma and the now tetrahedral carbon of the inhibitor. The decreased binding ability of thrombin inhibitors containing N-terminal acetylation is discussed as is the effect of replacing the P3 (D)phenylalanine with (D)cyclohexylalanine. The electron density surrounding the remainder of the inhibitor is generally well defined, the exceptions being the C-terminal (D)Glu, the highly flexible tetraglycine linker, and some of the solvent-directed side chains.(ABSTRACT TRUNCATED AT 250 WORDS)


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec.




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
P596 Inhibitor peptide
I
18N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
AR0
Query on AR0
I
peptide-likeC14 H25 N5 O3

--

ALC
Query on ALC
I
L-PEPTIDE LINKINGC9 H17 N O2ALA
DGL
Query on DGL
I
D-PEPTIDE LINKINGC5 H9 N O4

--

ZAL
Query on ZAL
I
D-peptide linkingC9 H17 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.600α = 90.00
b = 72.200β = 100.40
c = 72.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-10
    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