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- PDB-6t9u: Bovine Trypsine in complex with the synthetic inhibitor (S)-3'-(N... -

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Basic information

Entry
Database: PDB / ID: 6t9u
TitleBovine Trypsine in complex with the synthetic inhibitor (S)-3'-(N-(1-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-3-(3-carbamimidoylphenyl)-1-oxopropan-2-yl)sulfamoyl)-[1,1'-biphenyl]-3-carboximidamide (MI-490)
ComponentsCationic Trypsin
KeywordsHYDROLASE / Trypsin
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-MZE / trifluoroacetic acid / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.0675090501 Å
AuthorsMueller, J.M. / Merkl, S. / Keils, A. / Pilgram, O. / Steinmetzer, T.
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors
Authors: Pilgram, O. / Keils, A. / Benary, G.E. / Muller, J. / Merkl, S. / Ngaha, S. / Huber, S. / Chevillard, F. / Harbig, A. / Magdolen, V. / Heine, A. / Bottcher-Friebertshauser, E. / Steinmetzer, T.
History
DepositionOct 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 7, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Model completeness
Details: The ligand was added as a trifluoroacetic acid salt, the trifluoroacetic acid ion was missing from the original model. After its placement, the model was then refined again.
Provider: author / Type: Coordinate replacement
Revision 2.1Jun 1, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7636
Polymers25,8061
Non-polymers9575
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-12 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.631, 55.631, 109.764
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cationic Trypsin


Mass: 25806.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 243 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-MZE / 1-~{tert}-butyl-3-[1-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-(3-carbamimidoylphenyl)phenyl]sulfonylamino]propanoyl]piperidin-4-yl]urea


Mass: 646.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H42N8O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#6: 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

Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 100 mM Imidazole pH 8.0, 100 mM Ammoniumsulfate, 20-25 % PEG8000, 0.1% Sodiumazide, 1 mM Ligand, Protein at 10-20 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.0675090501→48.18 Å / Num. obs: 87632 / % possible obs: 99.6 % / Redundancy: 7.47 % / Biso Wilson estimate: 8.87108352395 Å2 / CC1/2: 0.999 / Rsym value: 0.05 / Net I/σ(I): 20.02
Reflection shellResolution: 1.07→1.13 Å / Redundancy: 7.26 % / Mean I/σ(I) obs: 3.61 / Num. unique obs: 13831 / CC1/2: 0.929 / Rsym value: 0.475 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2zfs

2zfs


Resolution: 1.0675090501→48.1778592379 Å / SU ML: 0.109780005075 / Cross valid method: FREE R-VALUE / σ(F): 1.36233264543 / Phase error: 11.950987472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.151480650244 4381 4.9997146933 %
Rwork0.135072512213 83244 -
obs0.135922105462 87625 99.5648122898 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.8165998026 Å2
Refinement stepCycle: LAST / Resolution: 1.0675090501→48.1778592379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 55 238 1908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842027480331854
X-RAY DIFFRACTIONf_angle_d1.088213480582552
X-RAY DIFFRACTIONf_chiral_restr0.0971716411235278
X-RAY DIFFRACTIONf_plane_restr0.00786792000697360
X-RAY DIFFRACTIONf_dihedral_angle_d14.3879302847694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0675090501-1.07960.4546197506781310.4509108909812497X-RAY DIFFRACTION91.8881118881
1.0796-1.09230.3014241457031440.3085928959462750X-RAY DIFFRACTION99.7931034483
1.0923-1.10570.2193037578061450.2221705907022753X-RAY DIFFRACTION99.8277643817
1.1057-1.11970.1943279172881450.180146611182746X-RAY DIFFRACTION99.8963372495
1.1197-1.13440.186599921611440.1422697678662745X-RAY DIFFRACTION99.861735223
1.1344-1.14990.1530551047181450.125779145082750X-RAY DIFFRACTION99.7587870434
1.1499-1.16640.1463165362271440.119603977132744X-RAY DIFFRACTION99.9307958478
1.1664-1.18380.1404433514721470.1142430218582786X-RAY DIFFRACTION99.9318568995
1.1838-1.20230.1434846200681440.1171022532552725X-RAY DIFFRACTION99.8955431755
1.2023-1.2220.1491667182091440.1189469498132752X-RAY DIFFRACTION99.9654815326
1.222-1.24310.13097057431460.1162049000252759X-RAY DIFFRACTION99.9655884377
1.2431-1.26570.1416444869181470.1167694799452804X-RAY DIFFRACTION100
1.2657-1.290.1303281073791440.1161274566212733X-RAY DIFFRACTION99.9652536484
1.29-1.31630.1260245357741460.1141282174652764X-RAY DIFFRACTION99.9656475438
1.3163-1.3450.1468981063771450.1140913682162755X-RAY DIFFRACTION100
1.345-1.37630.130933537151460.1107844441442792X-RAY DIFFRACTION99.9659748214
1.3763-1.41070.142433374981460.1108580980192759X-RAY DIFFRACTION99.9312005504
1.4107-1.44880.1316132781971460.1079992897522782X-RAY DIFFRACTION99.9658586548
1.4488-1.49150.1303979902991460.1074617374962766X-RAY DIFFRACTION99.9656711294
1.4915-1.53960.1245664057281470.1115409413112802X-RAY DIFFRACTION100
1.5396-1.59460.1247990594661470.1098223630712798X-RAY DIFFRACTION99.9660556687
1.5946-1.65850.1303357526331460.114323617632764X-RAY DIFFRACTION99.9656475438
1.6585-1.7340.1412937207681480.1147715140052818X-RAY DIFFRACTION99.9326145553
1.734-1.82540.1315052776521460.1223485979732774X-RAY DIFFRACTION99.9657651489
1.8254-1.93980.1397825663341470.1232913859162795X-RAY DIFFRACTION99.4590939824
1.9398-2.08950.1489211660531490.1251475015832824X-RAY DIFFRACTION99.8321020819
2.0895-2.29980.1431305532711490.1340548725432832X-RAY DIFFRACTION99.9329534026
2.2998-2.63260.1399159662581490.1391926737272838X-RAY DIFFRACTION99.8996655518
2.6326-3.31660.1709358785211520.1508364290662876X-RAY DIFFRACTION99.6380388286
3.3166-48.17785923790.1664512303121560.1562753211012961X-RAY DIFFRACTION98.0497011639

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