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- PDB-1lhg: HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BOROORNITHINE-OH -

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Basic information

Entry
Database: PDB / ID: 1lhg
TitleHUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BOROORNITHINE-OH
Components
  • (ALPHA-THROMBIN) x 2
  • HIRUDIN
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / BLOOD COAGULATION / PLASMA / CALCIUM-BINDING / GLYCOPROTEIN / DUPLICATION / VITAMIN K / ZYMOGEN / GAMMA-CARBOXYGLUTAMIC ACID / ACUTE PHASE / LIVER / HYDROLASE / SERINE PROTEASE / KRINGLE / DISEASE MUTATION / COMPLEX (SERINE PROTEASE-INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / cytolysis by host of symbiont cells / thrombin / regulation of blood coagulation / blood coagulation, common pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / cytolysis by host of symbiont cells / thrombin / regulation of blood coagulation / blood coagulation, common pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of fibrinolysis / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Peptide ligand-binding receptors / regulation of cytosolic calcium ion concentration / positive regulation of receptor signaling pathway via JAK-STAT / zymogen activation / positive regulation of release of sequestered calcium ion into cytosol / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Thrombin signalling through proteinase activated receptors (PARs) / serine-type endopeptidase complex / Regulation of Complement cascade / lipopolysaccharide binding / acute-phase response / Cell surface interactions at the vascular wall / negative regulation of proteolysis / growth factor activity / response to wounding / positive regulation of protein localization to nucleus / platelet activation / Golgi lumen / positive regulation of reactive oxygen species metabolic process / G alpha (q) signalling events / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / positive regulation of phosphatidylinositol 3-kinase signaling / heparin binding / positive regulation of cell growth / regulation of cell shape / collagen-containing extracellular matrix / blood microparticle / antimicrobial humoral immune response mediated by antimicrobial peptide / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / proteolysis / signaling receptor binding / serine-type endopeptidase activity / endoplasmic reticulum lumen / calcium ion binding / positive regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin light chain / Prothrombin/thrombin / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle domain / Kringle, conserved site / Kringle domain signature. / Kringle domain profile. / Kringle superfamily ...Thrombin light chain / Prothrombin/thrombin / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle domain / Kringle, conserved site / Kringle domain signature. / Kringle domain profile. / Kringle superfamily / Kringle / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Kringle-like fold / 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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / 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
AC-(D)PHE-PRO-BOROHOMOORNITHINE-OH / Prothrombin
Similarity search - Component
Biological speciesHirudo medicinalis (medicinal leech)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsWeber, P.C. / Lee, S.L. / Lewandowski, F.A. / Schadt, M.C. / Chang, C.H. / Kettner, C.A.
CitationJournal: Biochemistry / Year: 1995
Title: Kinetic and crystallographic studies of thrombin with Ac-(D)Phe-Pro-boroArg-OH and its lysine, amidine, homolysine, and ornithine analogs.
Authors: Weber, P.C. / Lee, S.L. / Lewandowski, F.A. / Schadt, M.C. / Chang, C.W. / Kettner, C.A.
History
DepositionDec 27, 1994-
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ALPHA-THROMBIN
H: ALPHA-THROMBIN
I: HIRUDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7644
Polymers35,3453
Non-polymers4181
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.400, 72.200, 72.200
Angle α, β, γ (deg.)90.00, 100.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide ALPHA-THROMBIN


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00734, thrombin
#2: Protein ALPHA-THROMBIN


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00734, thrombin
#3: Protein/peptide HIRUDIN /


Mass: 1468.517 Da / Num. of mol.: 1 / Fragment: RESIDUES 54 - 65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech)
#4: Chemical ChemComp-DI5 / AC-(D)PHE-PRO-BOROHOMOORNITHINE-OH


Mass: 418.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31BN4O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN IDENTIFIER *H* IS USED FOR RESIDUES 16 - 247. CHAIN IDENTIFIER *I* IS USED FOR THE 12-RESIDUE HIRUDIN PEPTIDE.
Sequence detailsCHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT ...CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8, 3467-3475).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop / Details: Skrzypczak, J., (1991) J. Mol. Biol., 221, 1379.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.0-3.7 mg/mlprotein1drop
20.05 Msodium phosphate1drop
30.375 M1dropNaCl
40.5 mM1dropNaN3
50.1 Msodium phospahte1reservoir
61-2 mM1reservoirNaN3
725-30 %(v/v)PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.25 Å / Rmerge(I) obs: 0.064

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.25→6 Å /
RfactorNum. reflection
obs0.195 11468
Refinement stepCycle: LAST / Resolution: 2.25→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 30 122 2440
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.021
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.018
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_restr0.173
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(I): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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