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- PDB-1gj6: ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER19... -

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Basic information

Entry
Database: PDB / ID: 1gj6
TitleENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE / selectivity at S1 / H2O displacement / uPA / tPA / Ser190/Ala190 protease / structure-based drug design
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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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-132 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsKatz, B.A. / Sprengeler, P.A. / Luong, C. / Verner, E. / Spencer, J.R. / Breitenbucher, J.G. / Hui, H. / McGee, D. / Allen, D. / Martelli, A. / Mackman, R.L.
CitationJournal: Chem.Biol. / Year: 2001
Title: Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets.
Authors: Katz, B.A. / Sprengeler, P.A. / Luong, C. / Verner, E. / Elrod, K. / Kirtley, M. / Janc, J. / Spencer, J.R. / Breitenbucher, J.G. / Hui, H. / McGee, D. / Allen, D. / Martelli, A. / Mackman, R.L.
History
DepositionApr 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2002Provider: 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: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7273
Polymers23,3241
Non-polymers4032
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.72, 63.08, 69.50
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein BETA-TRYPSIN / E.C.3.4.21.4


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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-132 / 6-CHLORO-2-(2-HYDROXY-BIPHENYL-3-YL)-1H-INDOLE-5-CARBOXAMIDINE


Mass: 362.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17ClN3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.1
Details: magnesium sulfate soak at pH 9.05, vapor diffusion at 298 K, pH 8.10
Crystal grow
*PLUS
pH: 7.5 / Method: batch method / Details: Katz, B.A., (2000) Chem.Biol., 7, 299.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 mM11Zn2+
21.51 M11MgSO4-7H2O
30.59 mMtrypsin11
45.0 %(v/v)DMSO11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.38→46.97 Å / Num. all: 58194 / Num. obs: 32043 / % possible obs: 55.1 % / Observed criterion σ(I): 0.8 / Redundancy: 2.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.7
Reflection shellResolution: 1.55→1.57 Å / Rmerge(I) obs: 0.266 / Num. unique all: 664 / % possible all: 37.1
Reflection
*PLUS
Num. obs: 30523 / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
X-PLOR3.851refinement
bioteXdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→7 Å / σ(F): 1.6 / Stereochemistry target values: X-PLOR force field
Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Ser110, Ser113, Ser130, Lys159, Asp165, Ser170, Gln175, Ser217, Lys230, Ser236, Ser244 Note that ...Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Ser110, Ser113, Ser130, Lys159, Asp165, Ser170, Gln175, Ser217, Lys230, Ser236, Ser244 Note that HOH383 makes short H-bonds to OgSer195 and O6' of the inhibitor Disordered waters are: HOH249 which is close to HOH250; HOH372 which is close to HOH373; HOH397 which is close to HOH398; HOH399 which is close to HOH400; sulfate_458 which is close to HOH459; HOH536 which is close to HOH537; HOH647 which is close to HOH648; HOH667 which is close to HOH668; HOH679 which is close to HOH680; HOH684 which is close to HOH685; HOH797 which is close to HOH798 which is close to HOH799; HOH902 which is close to HOH903; HOH947 which is close to HOH948; His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonated.
RfactorNum. reflection% reflection
Rfree0.206 3640 10 %
Rwork0.187 --
obs0.189 30523 67.7 %
all-45086 -
Refinement stepCycle: LAST / Resolution: 1.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 43 915 4307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg3.5
Refinement
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 10 % / Rfactor all: 0.189 / Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rwork: 0.189 / Rfactor obs: 0.189

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