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- PDB-4y0y: Trypsin in complex with with BPTI -

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Basic information

Entry
Database: PDB / ID: 4y0y
TitleTrypsin in complex with with BPTI
Components
  • Cationic trypsin
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE\INHIBITOR / HYDROLASE INHIBITORS / METAL-BINDING / SERINE PROTEASE / HYDROLASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular / 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 / 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
Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLoll, B. / Ye, S. / Berger, A.A. / Muelow, U. / Alings, C. / Wahl, M.C. / Koksch, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGraduate 25 School GRK 1582/1 Germany
CitationJournal: Chem Sci / Year: 2015
Title: Fluorine teams up with water to restore inhibitor activity to mutant BPTI.
Authors: Ye, S. / Loll, B. / Berger, A.A. / Mulow, U. / Alings, C. / Wahl, M.C. / Koksch, B.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 2.0Apr 18, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.label_alt_id / _atom_site.occupancy / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,94114
Polymers29,8522
Non-polymers1,08912
Water6,197344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-126 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.800, 81.490, 124.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules EI

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: residues 24-246 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Plasmid details: purchased / References: UniProt: P00760, trypsin
#2: Protein Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPTI


Mass: 6527.568 Da / Num. of mol.: 1 / Fragment: residues 36-93 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P00974

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Non-polymers , 4 types, 356 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 1.8 to 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 3, 2012
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.25→37 Å / Num. obs: 104119 / % possible obs: 99.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 18.7
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.7 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FTL

2ftl


Resolution: 1.25→36.912 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1552 5203 5 %Random selection
Rwork0.1378 ---
obs0.1387 104058 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→36.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 58 344 2485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162435
X-RAY DIFFRACTIONf_angle_d1.7233344
X-RAY DIFFRACTIONf_dihedral_angle_d12.213916
X-RAY DIFFRACTIONf_chiral_restr0.106362
X-RAY DIFFRACTIONf_plane_restr0.009430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2499-1.26410.38221600.35133055X-RAY DIFFRACTION93
1.2641-1.2790.31271670.29983159X-RAY DIFFRACTION96
1.279-1.29460.26431690.2663215X-RAY DIFFRACTION97
1.2946-1.3110.28161690.25543214X-RAY DIFFRACTION100
1.311-1.32830.23951740.20743306X-RAY DIFFRACTION100
1.3283-1.34650.25121720.20693275X-RAY DIFFRACTION100
1.3465-1.36570.22511740.20093299X-RAY DIFFRACTION100
1.3657-1.38610.23711740.19043299X-RAY DIFFRACTION100
1.3861-1.40770.19151730.16723283X-RAY DIFFRACTION100
1.4077-1.43080.18381720.15423281X-RAY DIFFRACTION100
1.4308-1.45550.14831730.14373288X-RAY DIFFRACTION100
1.4555-1.4820.17121740.14663297X-RAY DIFFRACTION100
1.482-1.51050.12971730.13253288X-RAY DIFFRACTION100
1.5105-1.54130.19971730.14623287X-RAY DIFFRACTION100
1.5413-1.57480.14771730.12283282X-RAY DIFFRACTION100
1.5748-1.61140.14441720.11213283X-RAY DIFFRACTION100
1.6114-1.65170.15561750.11183321X-RAY DIFFRACTION100
1.6517-1.69640.15341740.1063309X-RAY DIFFRACTION100
1.6964-1.74630.14141730.11253278X-RAY DIFFRACTION100
1.7463-1.80270.13351750.11383332X-RAY DIFFRACTION100
1.8027-1.86710.16221750.11833325X-RAY DIFFRACTION100
1.8671-1.94190.13121740.12333297X-RAY DIFFRACTION100
1.9419-2.03020.14491750.11823329X-RAY DIFFRACTION100
2.0302-2.13730.12981750.11813333X-RAY DIFFRACTION100
2.1373-2.27120.12131740.11823297X-RAY DIFFRACTION100
2.2712-2.44650.15031760.12343343X-RAY DIFFRACTION100
2.4465-2.69260.14411760.13323354X-RAY DIFFRACTION100
2.6926-3.08210.16191770.14793362X-RAY DIFFRACTION100
3.0821-3.88240.14361790.13123393X-RAY DIFFRACTION100
3.8824-36.92830.1461830.14163471X-RAY DIFFRACTION98

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