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- PDB-4y10: Trypsin in complex with with BPTI mutant (2S)-2-amino-4,4-difluor... -

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Basic information

Entry
Database: PDB / ID: 4y10
TitleTrypsin in complex with with BPTI mutant (2S)-2-amino-4,4-difluorobutanoic acid
Components
  • Cationic trypsin
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE INHIBITORS / DIGESTION / METAL-BINDING / PROTEASE / SECRETED / SERINE PROTEASE / ZYMOGEN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / 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 / potassium channel inhibitor activity / negative regulation of platelet aggregation / 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 / protease binding / endopeptidase activity / 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 ...: / 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: 1.37 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 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 / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...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_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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)30,84113
Polymers29,8442
Non-polymers99711
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-128 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.694, 81.854, 123.612
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 / trypsin


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


Mass: 6519.474 Da / Num. of mol.: 1 / Fragment: UNP residues 36-93 / Source method: obtained synthetically / Details: non-canonical amino acid incorporated (OBF) / Source: (synth.) Bos taurus (cattle) / References: UniProt: P00974

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Non-polymers , 4 types, 357 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.: 1 / 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.: 346 / 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: 61.14 %
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: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 79871 / % possible obs: 99.6 % / Redundancy: 8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.2
Reflection shellResolution: 1.37→1.48 Å / Redundancy: 8 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→34.124 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1652 3992 5 %Random selection
Rwork0.138 ---
obs0.1393 79833 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→34.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 52 346 2469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192330
X-RAY DIFFRACTIONf_angle_d1.6913177
X-RAY DIFFRACTIONf_dihedral_angle_d11.95864
X-RAY DIFFRACTIONf_chiral_restr0.1343
X-RAY DIFFRACTIONf_plane_restr0.011408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3669-1.3830.26581300.25142471X-RAY DIFFRACTION94
1.383-1.39990.25561340.22452554X-RAY DIFFRACTION100
1.3999-1.41760.26561370.21442594X-RAY DIFFRACTION100
1.4176-1.43620.26311370.2012620X-RAY DIFFRACTION100
1.4362-1.45590.25211380.17822612X-RAY DIFFRACTION100
1.4559-1.47670.22441360.17162578X-RAY DIFFRACTION100
1.4767-1.49880.18841360.16182590X-RAY DIFFRACTION100
1.4988-1.52220.18391370.15222594X-RAY DIFFRACTION100
1.5222-1.54710.17231370.15162615X-RAY DIFFRACTION100
1.5471-1.57380.20381360.14962579X-RAY DIFFRACTION100
1.5738-1.60240.15281370.13672615X-RAY DIFFRACTION100
1.6024-1.63320.1751390.13422623X-RAY DIFFRACTION100
1.6332-1.66660.16881360.12792592X-RAY DIFFRACTION100
1.6666-1.70280.15171370.12382603X-RAY DIFFRACTION100
1.7028-1.74240.15371380.12512613X-RAY DIFFRACTION100
1.7424-1.7860.14321360.12622603X-RAY DIFFRACTION100
1.786-1.83430.17681370.12352600X-RAY DIFFRACTION100
1.8343-1.88830.16171380.12512613X-RAY DIFFRACTION99
1.8883-1.94920.14451380.12622629X-RAY DIFFRACTION100
1.9492-2.01890.161380.12442611X-RAY DIFFRACTION100
2.0189-2.09970.16261370.12422611X-RAY DIFFRACTION100
2.0997-2.19520.16331380.12222625X-RAY DIFFRACTION100
2.1952-2.31090.14181380.12362626X-RAY DIFFRACTION100
2.3109-2.45570.14791390.12922626X-RAY DIFFRACTION100
2.4557-2.64520.13791390.13222642X-RAY DIFFRACTION100
2.6452-2.91130.17261390.14362652X-RAY DIFFRACTION100
2.9113-3.33230.18031410.13852672X-RAY DIFFRACTION100
3.3323-4.19710.12541410.12292690X-RAY DIFFRACTION100
4.1971-34.13440.18491480.15412788X-RAY DIFFRACTION99

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