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- PDB-1lqe: CRYSTAL STRUCTURE OF TRYPSIN IN COMPLEX WITH 79. -

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Basic information

Entry
Database: PDB / ID: 1lqe
TitleCRYSTAL STRUCTURE OF TRYPSIN IN COMPLEX WITH 79.
ComponentsTRYPSIN
KeywordsHYDROLASE / Factor Xa inhibitor / enzyme-inhibitor complex / blood coagulation factor / serine proteinase
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
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 ...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
Chem-IMA / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchreuder, H.A. / Liesum, A.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Design and quantitative structure-activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa.
Authors: Matter, H. / Defossa, E. / Heinelt, U. / Blohm, P.M. / Schneider, D. / Mueller, A. / Herok, S. / Schreuder, H.A. / Liesum, A. / Brachvogel, V. / Loenze, P. / Walser, A. / Al-Obeidi, F. / Wildgoose, P.
History
DepositionMay 10, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1284
Polymers25,4451
Non-polymers6833
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.600, 63.600, 68.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPSIN / / BETA-TRYPSIN


Mass: 25444.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IMA / [4-({[5-BENZYLOXY-1-(3-CARBAMIMIDOYL-BENZYL)-1H-INDOLE-2-CARBONYL]-AMINO}-METHYL)-PHENYL]-TRIMETHYL-AMMONIUM


Mass: 546.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36N5O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / PH range low: 7 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.6 mMammonium sulfate1drop
21 mg/ml1dropCaCl2
310 mg/mlbenzamidine1drop
460 mg/mlprotein1drop
51.2-1.6 Mammonium sulfate1reservoir
61reservoirNaOHpH5.0-7.0

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54128 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 9, 1996 / Details: Graphite monochromator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54128 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. all: 14711 / Num. obs: 14008 / % possible obs: 95.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.098 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 6 / Num. unique all: 1812 / Rsym value: 0.268 / % possible all: 94
Reflection
*PLUS
Num. measured all: 45455 / Rmerge(I) obs: 0.098

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLORmodel building
X-PLOR3.1refinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→8 Å / Isotropic thermal model: Isotropic / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
all0.166 14711 -
obs0.166 14008 95.2 %
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 39 139 1807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_dihedral_angle_d16.4
X-RAY DIFFRACTIONx_improper_angle_d1.35
Refinement
*PLUS
Highest resolution: 2.2 Å / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35

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