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- PDB-1c1p: RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE ... -

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Basic information

Entry
Database: PDB / ID: 1c1p
TitleRECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES
ComponentsTRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ZN(II)-MEDIATED SERINE PROTEASE INHIBITORS / PH DEPENDENCE / ZN(II) AFFINITY STUCTURE-BASED DRUG DESIGN / SERINE PROTEASE SERINE PROTEASE/INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / proteolysis / serine-type endopeptidase activity / extracellular space / metal ion binding
Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain / Peptidase S1, PA clan, chymotrypsin-like fold / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site / Peptidase S1, PA clan / Trypsin-like serine proteases / Thrombin, subunit H / Beta Barrel / Mainly Beta
Cationic trypsin
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER PLUS REFINEMENT / Resolution: 1.37 Å
AuthorsKatz, B.A. / Luong, C.
CitationJournal: Nature / Year: 1998
Title: Design of potent selective zinc-mediated serine protease inhibitors.
Authors: Katz, B.A. / Clark, J.M. / Finer-Moore, J.S. / Jenkins, T.E. / Johnson, C.R. / Ross, M.J. / Luong, C. / Moore, W.R. / Stroud, R.M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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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)23,9497
Polymers23,3241
Non-polymers6256
Water4,288238
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)54.860, 54.860, 109.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-870-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TRYPSIN /


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMPLEXED WITH (5-AMIDINO-2-BENZIMIDAZOLYL)(2-BENZIMIDAZOLYL)METHANE
Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 6 types, 244 molecules

#2: Chemical ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BAI / (5-AMIDINO-2-BENZIMIDAZOLYL)(2-BENZIMIDAZOLYL)METHANE / HEMI-BABIM


Mass: 290.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N6
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsHIS91 IS MONOPROTONATED ON THE EPSILON NITROGEN. HIS40 AND HIS57 ARE DOUBLY PROTONATED.

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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: 2.04 Å3/Da / Density % sol: 18 %
Crystal growpH: 5.9
Details: TRYPSIN-BENZAMIDINE, P3(1) 2 1 WERE GROWN BY VAPOR DIFFUSION, AS DESCRIBED FOR P2(1) 2(1) 2(1) (LARGE CELL) (MANGEL, ET AL., BIOCHEMISTRY 29, 8351-8357, 1990) THE CRYSTAL WAS SOAKED IN A ...Details: TRYPSIN-BENZAMIDINE, P3(1) 2 1 WERE GROWN BY VAPOR DIFFUSION, AS DESCRIBED FOR P2(1) 2(1) 2(1) (LARGE CELL) (MANGEL, ET AL., BIOCHEMISTRY 29, 8351-8357, 1990) THE CRYSTAL WAS SOAKED IN A SOLUTION OF 0.10 M MES, 2.02 M MGSO4 . 7 H2O, PH 5.90, 2.0 % DMSO, SATURATED IN HEMI-BABIM OVER A PERIOD OF SEVERAL DAYS WITH SEVERAL REPLACEMENTS OF THE SOAKING SOLUTION.
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 26, 1998 / Details: MSC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.33→35.94 Å / Num. obs: 35904 / % possible obs: 86 % / Observed criterion σ(I): 0.9 / Redundancy: 3.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5
Reflection shellResolution: 1.37→1.43 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.1 / % possible all: 41.4

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Processing

Software
NameVersionClassification
bioteX(MSC)data collection
bioteX(MSC)data reduction
X-PLORmodel building
Quantamodel building
Insight IImodel building
X-PLOR3.1refinement
bioteXdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER PLUS REFINEMENT
Resolution: 1.37→7.5 Å / Cross valid method: X-PLOR / σ(F): 1.8
Details: BULK SOLVENT TERMS INCLUDED IN FOB FILE CREATED WITH STANDARD X-PLOR SCRIPT.
RfactorNum. reflection% reflection
Rfree0.192 3486 10 %
Rwork0.178 --
Obs0.178 35068 86 %
Refinement stepCycle: LAST / Resolution: 1.37→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 59 714 4092
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.37→1.43 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.48 213 10 %
Rwork0.458 1848 -
Obs--41.4 %
Xplor file
Refinement-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARMALLH3X_TR1706SUL.PROTOPALLH6X_TR1706SUL.PRO
X-RAY DIFFRACTION2PARAM11_UCSF.WAT

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