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- PDB-1c5s: STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING,... -

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Basic information

Entry
Database: PDB / ID: 1c5s
TitleSTRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR
ComponentsPROTEIN (TRYPSIN)
KeywordsHYDROLASE / selective / S1 site inhibitor / structure-based drug design / urokinase / trypsin / thrombin
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
BENZO[B]THIOPHENE-2-CARBOXAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER PLUS REFINEMENT / Resolution: 1.36 Å
AuthorsKatz, B.A. / Mackman, R. / Luong, C. / Radika, K. / Martelli, A. / Sprengeler, P.A. / Wang, J. / Chan, H. / Wong, L.
CitationJournal: Chem.Biol. / Year: 2000
Title: Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator.
Authors: Katz, B.A. / Mackman, R. / Luong, C. / Radika, K. / Martelli, A. / Sprengeler, P.A. / Wang, J. / Chan, H. / Wong, L.
History
DepositionDec 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 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
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_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 / _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 2.1Oct 30, 2024Group: Advisory / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (TRYPSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1189
Polymers23,3241
Non-polymers7948
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.030, 55.030, 109.210
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-377-

HOH

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Components

#1: Protein PROTEIN (TRYPSIN)


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / 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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ESX / BENZO[B]THIOPHENE-2-CARBOXAMIDINE


Mass: 177.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.05 Å3/Da / Density % sol: 18 %
Crystal growMethod: vapor diffusion / pH: 8.2
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 85 % saturated MgSO4 . 7 H2O, 100 mM Tris, 1 mM CaCl2, 2.0 % DMSO,saturated with inhibitor, pH 8.20 over a period of several days with several replacements of the soaking solution., VAPOR DIFFUSION
Crystal grow
*PLUS
pH: 7.5 / Method: batch method / Details: Katz, B.A., (1999) J. Mol. Biol., 292, 669.
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 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 18, 1997 / 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→35.91 Å / Num. all: 37545 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.0502 / Net I/σ(I): 13.6
Reflection shellResolution: 1.36→1.42 Å / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.5 / % possible all: 50.4
Reflection
*PLUS
Highest resolution: 1.36 Å

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Processing

Software
NameVersionClassification
bioteX(MSC)data collection
bioteX(MSC)data reduction
X-PLOR3.1model building
Quantamodel building
Insight IImodel building
X-PLOR3.1refinement
bioteXdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER PLUS REFINEMENT
Resolution: 1.36→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. Residues simultaneously refined in two or more conformations are: Gln50, Met104, Ser110, Ser170, Ser236, Ile242 ...Details: Bulk solvent terms included in Fob file created with standard X-PLOR script. Residues simultaneously refined in two or more conformations are: Gln50, Met104, Ser110, Ser170, Ser236, Ile242 Disordered waters are: HOH285 which is close to HOH306; HOH292 which is close to HOH331; HOH318 which is close to HOH327; HOH329 which is close to HOH360; HOH338 which is close to a symmetry_related equivalent of itself; HOH377 which is close to a symmetry-related equivalent of itself; HOH482 which is close to a symmetry-related equivalent of itself. His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN HIS57 is monoprotonated on delta nitrogen.
RfactorNum. reflection% reflection
Rfree0.224 3693 10 %
Rwork0.197 --
obs0.197 36792 88 %
Refinement stepCycle: LAST / Resolution: 1.36→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 52 612 3934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_improper_angle_d0.58
LS refinement shellResolution: 1.36→1.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.448 254 -
Rwork0.417 2320 -
obs--50.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1tr7377_parmallh3x.protr7377_topallh6x.pro
X-RAY DIFFRACTION2tr7377_param11_ucsf.wat
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7.5 Å / σ(F): 1.8 / % reflection Rfree: 10 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.58
LS refinement shell
*PLUS
Rfactor Rfree: 0.448 / Rfactor Rwork: 0.417

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