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- PDB-1hrt: THE STRUCTURE OF A COMPLEX OF BOVINE ALPHA-THROMBIN AND RECOMBINA... -

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Basic information

Entry
Database: PDB / ID: 1hrt
TitleTHE STRUCTURE OF A COMPLEX OF BOVINE ALPHA-THROMBIN AND RECOMBINANT HIRUDIN AT 2.8 ANGSTROMS RESOLUTION
Components
  • HIRUDIN
  • THROMBIN (LARGE SUBUNIT)
  • THROMBIN (SMALL SUBUNIT)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of serine-type peptidase activity / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity ...negative regulation of serine-type peptidase activity / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Thrombin Inhibitor (Hirudin); Chain I / Thrombin Inhibitor (Hirudin), subunit I / Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain ...Thrombin Inhibitor (Hirudin); Chain I / Thrombin Inhibitor (Hirudin), subunit I / Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Distorted Sandwich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Prothrombin / Hirudin variant-1
Similarity search - Component
Biological speciesBos taurus (cattle)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsVitali, J. / Edwards, B.F.P.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: The structure of a complex of bovine alpha-thrombin and recombinant hirudin at 2.8-A resolution.
Authors: Vitali, J. / Martin, P.D. / Malkowski, M.G. / Robertson, W.D. / Lazar, J.B. / Winant, R.C. / Johnson, P.H. / Edwards, B.F.
History
DepositionFeb 25, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: THROMBIN (SMALL SUBUNIT)
H: THROMBIN (LARGE SUBUNIT)
I: HIRUDIN


Theoretical massNumber of molelcules
Total (without water)42,4813
Polymers42,4813
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-25 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.110, 102.620, 143.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO H 37

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Components

#1: Protein/peptide THROMBIN (SMALL SUBUNIT)


Mass: 5735.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: unidentified (others) / References: UniProt: P00735, thrombin
#2: Protein THROMBIN (LARGE SUBUNIT)


Mass: 29772.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: unidentified (others) / References: UniProt: P00735, thrombin
#3: Protein HIRUDIN


Mass: 6973.505 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: unidentified (others) / References: UniProt: P01050
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *I* IS USED FOR HIRUDIN. THE COMPLEX CONSISTS OF ONE MOLECULE OF ALPHA-THROMBIN AND ONE MOLECULE OF HIRUDIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
129 %PEG40001reservoir
2250 mMsodium phosphate1reservoir
394 mM1reservoirNaCl
40.005 %1reservoirNaN3
57 mg/mlthrombin-hirudin1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 9999 Å / Num. obs: 7688 / Observed criterion σ(I): 1 / Num. measured all: 19008 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.8 Å / % possible obs: 13 %

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.8→7 Å / σ(F): 0
Details: SUBSEQUENT TO PUBLICATION, ADDITIONAL REFINEMENT WAS CARRIED OUT WITH PROFFT USING DAMPING FACTORS OF 0.7 FOR BOTH POSITIONAL AND THERMAL PARAMETERS. THE USE OF THIS DAMPING FACTOR COMPARED ...Details: SUBSEQUENT TO PUBLICATION, ADDITIONAL REFINEMENT WAS CARRIED OUT WITH PROFFT USING DAMPING FACTORS OF 0.7 FOR BOTH POSITIONAL AND THERMAL PARAMETERS. THE USE OF THIS DAMPING FACTOR COMPARED TO THE FULL SHIFTS APPLIED EARLIER REDUCED THE R VALUE FROM 0.161 REPORTED IN THE PAPER TO 0.155. THIS ENTRY CONTAINS THE REVISED COORDINATES. THESE COORDINATES GIVE THE SAME DISTANCES (WITHIN 0.2 ANGSTROMS) AS THOSE DISCUSSED IN THE PAPER.
RfactorNum. reflection
obs0.155 6958
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 0 129 2996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d0.041
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.148
X-RAY DIFFRACTIONp_singtor_nbd0.22
X-RAY DIFFRACTIONp_multtor_nbd0.33
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.35
X-RAY DIFFRACTIONp_planar_tor2.7
X-RAY DIFFRACTIONp_staggered_tor24
X-RAY DIFFRACTIONp_orthonormal_tor29.9
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 7 Å / Num. reflection all: 6958 / σ(F): 0 / Rfactor all: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS

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