4THN

THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode.

Lombardi, A.De Simone, G.Nastri, F.Galdiero, S.Della Morte, R.Staiano, N.Pedone, C.Bolognesi, M.Pavone, V.

(1999) Protein Sci. 8: 91-95

  • DOI: 10.1110/ps.8.1.91

  • PubMed Abstract: 
  • The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 A resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which jus ...

    The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 A resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which justifies the high inhibitory potency and the selectivity of hirunorm IV. This novel inhibitor, composed of 26 amino acids, interacts through the N-terminal end with the alpha-thrombin active site in a nonsubstrate mode, and binds specifically to the fibrinogen recognition exosite through the C-terminal end. The backbone of the N-terminal tripeptide Chg1"-Arg2"-2Na13" (Chg, cyclohexyl-glycine; 2Na1, beta-(2-naphthyl)-alanine) forms a parallel beta-strand to the thrombin main-chain segment Ser214-Gly216. The Chg1" side chain occupies the S2 site, Arg2" penetrates into the S1 specificity site, while the 2Na13" side chain occupies the aryl binding site. The Arg2" side chain enters the S1 specificity pocket from a position quite apart from the canonical P1 site. This notwithstanding, the Arg2" side chain establishes the typical ion pair with the carboxylate group of Asp189.


    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 2D, J.W.
      (1990) Science 249: 277
    • Rational Design of True Hirudin Mimetics: Synthesis and Characterization of Multisite-Directed Alpha-Thrombin Inhibitors
      Lombardi, A.,Nastri, F.,Della Morte, R.,Rossi, A.,De Rosa, A.,Staiano, N.,Pedone, C.,Pavone, V.
      (1996) J.Med.Chem. 39: 2008
    • Refined Structure of the Hirudin-Thrombin Complex
      Rydel, T.J.,Tulinsky, A.,Bode, W.,Huber, R.
      (1991) J.Mol.Biol. 221: 583
    • Hirunorms are True Hirudin Mimetics. The Crystal Structure of Human Alpha-Thrombin-Hirunorm V Complex
      De Simone, G.,Lombardi, A.,Galdiero, S.,Nastri, F.,Della Morte, R.,Staiano, N.,Pedone, C.,Bolognesi, M.,Pavone, V.
      (1998) Protein Sci. 7: 243


    Organizational Affiliation

    Centro Interuniversitario di Ricerca su Peptidi Bioattivi & Centro di Studio di Biocristallografia-CNR, University of Napoli Federico II, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN
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
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
HIRUNORM IV
I
26N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
BAL
Query on BAL
I
peptide-likeC3 H7 N O2

--

NAL
Query on NAL
I
L-PEPTIDE LINKINGC13 H13 N O2ALA
HMF
Query on HMF
I
D-PEPTIDE LINKINGC10 H13 N O2

--

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

--

AIB
Query on AIB
I
L-PEPTIDE LINKINGC4 H9 N O2ALA
DAL
Query on DAL
I
D-PEPTIDE LINKINGC3 H7 N O2

--

CHG
Query on CHG
I
L-PEPTIDE LINKINGC8 H15 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.300α = 90.00
b = 72.700β = 100.00
c = 73.600γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
MOSFLMdata reduction
CCP4data reduction
CCP4phasing
CCP4model building
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    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