1DOJ

Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.217 (Depositor) 
  • R-Value Work: 
    0.174 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1Z0Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

Structure of human alpha-thrombin complexed with RWJ-51438 at 1.7 A: unusual perturbation of the 60A-60I insertion loop.

Recacha, R.Costanzo, M.J.Maryanoff, B.E.Carson, M.DeLucas, L.Chattopadhyay, D.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1395-1400

  • DOI: https://doi.org/10.1107/s0907444900010763
  • Primary Citation of Related Structures:  
    1DOJ

  • PubMed Abstract: 

    The three-dimensional structure of the ternary complex consisting of human alpha-thrombin, hirugen and the active-site inhibitor RWJ-51438 has been determined at 1.7 A resolution. The crystals of the complex belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 62.98, b = 117.52, c = 47.99 A. The refined R and R(free) values are 0.196 and 0.232, respectively. The ketone carbonyl group of the inhibitor is covalently linked to the hydroxyl O atom of Ser195, forming a tetrahedral intermediate hemiketal structure; the benzothiazole ring N atom of RWJ-51438 forms a hydrogen bond with His57. Surprisingly, the carboxylate substituent on the benzothiazole group forms salt bridges with Lys60F NZ and the NZ of the symmetry-related residues Lys236 and Lys240, which introduces steric effects that perturb the 60A-60I insertion loop, especially at residues Trp60D and Phe60H.


  • Organizational Affiliation

    Center for Macromolecular Crystallography, University of Alabama at Birmingham, Birmingham, Alabama 35294-0005, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-THROMBIN295Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P00734-1
Sequence Annotations
Expand
  • Reference Sequence
1DOJ_1
020406080100120140160180200220240260280
1DOJ_1
UNIPROT P00734
UNMODELED
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIRUGEN11N/AMutation(s): 0 
UniProt
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28504
Sequence Annotations
Expand
  • Reference Sequence
1DOJ_2
1234567891011
1DOJ_2
DFEEIPEEYLQ
UNIPROT P28504
DFEEIPEEYLQ
MODIFIED MONOMER
HYDROPATHY
DISORDER
DISORDERED BINDING
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.217 (Depositor) 
  • R-Value Work:  0.174 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.982α = 90
b = 117.521β = 90
c = 47.989γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1Z0Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.6: 2024-10-30
    Changes: Structure summary