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- PDB-1c1s: RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE ... -

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Basic information

Entry
Database: PDB / ID: 1c1s
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/INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsin / serpin family protein binding / digestion / serine protease inhibitor complex / 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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / 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. / 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
BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE / PHOSPHATE ION / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER PLUS REFINEMENT / Resolution: 1.63 Å
AuthorsKatz, B.A. / Luong, C.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Recruiting Zn2+ to mediate potent, specific inhibition of serine proteases.
Authors: Katz, B.A. / Luong, C.
History
DepositionJul 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Dec 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0087
Polymers23,3241
Non-polymers6836
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.350, 55.350, 109.800
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-1022-

HOH

21A-1152-

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 BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANE
Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 285 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-BAB / BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE


Mass: 335.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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 MONOPROTONATED ON THE DELTA NITROGEN.

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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: 2.08 Å3/Da / Density % sol: 18 %
Crystal growpH: 6.1
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 1.25 M NA2PO4 . 7 H2O, 1.75 M KH2PO4, 2.0 % DMSO, SATURATED IN BABIM OVER A PERIOD OF 5 DAYS WITH SEVERAL REPLACEMENTS OF THE SOAKING SOLUTION., pH 6.1
Crystal grow
*PLUS
pH: 8.15 / Method: vapor diffusion, hanging drop / Details: Mangel, W.F., (1990) Biochemistry, 29, 8351.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 mg/mltrypsin1drop
20.05 MTris-HCl1drop
30.3 M1dropMgSO4
40.006 M1dropCaCl2
50.06 Mbenzamidine1drop
61.3 mMenzyme1drop
70.05 MTris-HCl1reservoir
81.6-1.8 M1reservoirMgSO4

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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: Dec 16, 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→36.6 Å / Num. obs: 23706 / % possible obs: 67 % / Observed criterion σ(I): 0.9 / Redundancy: 2.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.3
Reflection shellResolution: 1.63→1.7 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 1.5 / % possible all: 41.8
Reflection
*PLUS
Redundancy: 2.4 % / Num. measured all: 56042

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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: 1.63→7.5 Å / Cross valid method: X-PLOR / σ(F): 2
Details: BULK SOLVENT TERMS INCLUDED IN FOB FILE CREATED WITH STANDARD X-PLOR SCRIPT.
RfactorNum. reflection% reflection
Rfree0.206 1657 10 %
Rwork0.185 --
obs0.185 16621 67 %
Refinement stepCycle: LAST / Resolution: 1.63→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 30 279 1938
Refine LS restraints
Refine-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_deg3.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.57
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: 1.63→1.7 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.411 123 10 %
Rwork0.367 1142 -
obs--41.8 %
Xplor fileSerial no: 1 / Param file: PARMALLH3X_TRBAB_PO4_61.P / Topol file: TOPALLH6X_TRBAB_PO4_61.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7.5 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.57
LS refinement shell
*PLUS
Lowest resolution: 1.7 Å / Rfactor Rfree: 0.411 / Rfactor Rwork: 0.186

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