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- PDB-1c5r: STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING,... -

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Basic information

Entry
Database: PDB / ID: 1c5r
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
4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE / CITRATE ANION / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER PLUS REFINEMENT / Resolution: 1.47 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 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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_atom_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_atom_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 16, 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: PROTEIN (TRYPSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0496
Polymers23,3241
Non-polymers7245
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.000, 55.000, 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-387-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 244 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 303.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8IN2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 18 %
Crystal growpH: 5.5
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 citrate, 1 mM CaCl2, 2.0 % DMSO, saturated with inhibitor, pH 5.50 over a period of several days with several replacements of the soaking solution.
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: Feb 17, 1999 / 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→28.92 Å / Num. all: 23913 / % possible obs: 66 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.4
Reflection shellResolution: 1.47→1.54 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.7 / % possible all: 33.9
Reflection
*PLUS
Highest resolution: 1.47 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: 1.47→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. Residues simultaneously refined in two or more conformations are: Gln50, Met104, Ser110, Ser170, Ser236 ...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 Disordered waters are: HOH283 which is close to HOH315; HOH387 which is close to a symmetry-related equivalent of itself; HOH597 which is close to a symmetry-related equivalent of itself. HOH364 WHICH IS CLOSE TO HOH437 WHICH IS CLOSE TO HOH360; HOH450 WHICH IS CLOSE TO HOH452 AND TO HOH465; HOH391 WHICH IS CLOSE TO HOH468; HOH473 WHICH IS CLOSE TO HOH472 AND HOH480; HOH410 WHICH IS CLOSE TO HOH411; HOH459 WHICH IS CLOSE TO HOH461; HOH462 WHICH IS CLOSE TO HOH465; HOH455 WHICH IS CLOSE TO A SYMMETRY-EQUIVALENT OF HOH456. HIS91 is MONOPROTONATED ON THE EPSILON NITROGEN His40 and HIS57 are DIPROTONATED.
RfactorNum. reflection% reflection
Rfree0.229 2152 10 %
Rwork0.192 --
obs0.192 21757 66 %
Refinement stepCycle: LAST / Resolution: 1.47→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 50 717 4026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_angle_deg3.9
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_improper_angle_d0.5
LS refinement shellResolution: 1.47→1.54 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.462 120 10 %
Rwork0.419 1262 -
obs--33.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1tr6860cit55_parmallh3x.protr6860cit55_topallh6x.pro
X-RAY DIFFRACTION2tr6860cit55_param11_ucsf.wat
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7.5 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.462 / % reflection Rfree: 10 % / Rfactor Rwork: 0.419

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