1VIT

THROMBIN:HIRUDIN 51-65 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

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This is version 2.0 of the entry. See complete history


Literature

Structure of a bovine thrombin-hirudin51-65 complex determined by a combination of molecular replacement and graphics. Incorporation of known structural information in molecular replacement.

Vitali, J.Martin, P.D.Malkowski, M.G.Olsen, C.M.Johnson, P.H.Edwards, B.F.

(1996) Acta Crystallogr D Biol Crystallogr 52: 453-464

  • DOI: 10.1107/S0907444996000364
  • Primary Citation of Related Structures:  
    1VIT

  • PubMed Abstract: 
  • Crystals of the bovine thrombin-hirudins(51-65) complex have space group P6(1)22 with cell constants a = 116.4, and c = 200.6 A and two thrombin molecules in the asymmetric unit. Only one thrombin molecule could be located by generalized molecular replacement; the second was fit visually as a rigid body to an improved electron-density difference map ...

    Crystals of the bovine thrombin-hirudins(51-65) complex have space group P6(1)22 with cell constants a = 116.4, and c = 200.6 A and two thrombin molecules in the asymmetric unit. Only one thrombin molecule could be located by generalized molecular replacement; the second was fit visually as a rigid body to an improved electron-density difference map. The structure was refined to R = 0.192 with two B values per residue (main chain and side chain) at 3.2 A. The polar interactions of the peptides with the exosite of thrombin show differences consistent with the known flexibility in the interactions of the C-terminal peptide of hirudin with thrombin. The hirudin peptide in complex 2 has a higher temperature factor as compared with peptide 1 which may be correlated partly with a larger number of short-range electrostatic interactions between peptide 1 and thrombin and partly with the fact that thrombin 2 is epsilon-thrombin which is cleaved at Thr149A near the peptide binding site. Later, using this structure as a test case, it was shown that the position for the second thrombin could also be determined by a novel modification of the molecular-replacement method in which the contribution of the known molecule is subtracted from the structure factors. This approach is facile and applicable to any crystal containing two or more macromolecules in the asymmetric unit in which some but not all of the molecules can be determined by molecular replacement.


    Organizational Affiliation

    Department of Biochemistry, Wayne State University, Detroit, MI 48201, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EPSILON THROMBINA [auth L], D [auth M]49Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA THROMBINB [auth H]259Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIRUDINC [auth I], G [auth J]15N/AMutation(s): 0 
UniProt
Find proteins for P28507 (Hirudo medicinalis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
EPSILON THROMBINE [auth F]150Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
EPSILON THROMBINF [auth G]109Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth A]2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth F]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.4α = 90
b = 116.4β = 90
c = 200.6γ = 120
Software Package:
Software NamePurpose
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary