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 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

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This is version 1.4 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: 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 ...

    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.

    Related Citations: 
    • 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 II, J.W.
      (1992) Biochemistry 31: 11689
    • Crystal Structure of Thrombin with Thiazole-Containing Inhibitors: Probes of the S1' Binding Site
      Matthews, J.H., Krishnan, R., Costanzo, M.J., Maryanoff, B.E., Tulinsky, A.
      (1996) Biophys J 71: 2830
    • The Refined 1.9-A X-ray Crystal Structure of D-Pro-Phe-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships
      Bode, W., Turk, D., Karshikov, A.
      (1992) Protein Sci 1: 426
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-THROMBIN A295Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIRUGEN B11N/AMutation(s): 0 
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1Z0
Query on 1Z0
Download Ideal Coordinates CCD File 
A
N-methyl-D-phenylalanyl-N-{(1S)-4-carbamimidamido-1-[(6-carboxy-1,3-benzothiazol-2-yl)carbonyl]butyl}-L-prolinamide
C29 H35 N7 O5 S
XNPQCHOSZVJBHP-BDTNDASRSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS		BL-PEPTIDE LINKINGC9 H11 N O6 STYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000623 (1Z0)
Query on PRD_000623		ARWJ-51438Peptide-like /  Thrombin inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • 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

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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