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- PDB-4y11: Trypsin in complex with with BPTI mutant (2S)-2-amino-4,4,4-trifl... -

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Basic information

Entry
Database: PDB / ID: 4y11
TitleTrypsin in complex with with BPTI mutant (2S)-2-amino-4,4,4-trifluorobutanoic acid
Components
  • Cationic trypsin
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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 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
Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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)30,95114
Polymers29,8622
Non-polymers1,08912
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-124 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.971, 82.102, 123.578
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: 6537.464 Da / Num. of mol.: 1 / Fragment: UNP residues 36-93 / Mutation: y / Source method: obtained synthetically / Details: non-canonical amino acid 3EG incorporated / Source: (synth.) Bos taurus (cattle) / References: UniProt: P00974

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Non-polymers , 4 types, 313 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.: 301 / 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

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.37 %
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
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 93017 / % possible obs: 99.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.8
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.9 / % possible all: 97.9

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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: 1.3→36.102 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.156 4649 5 %Random selection
Rwork0.1339 ---
obs0.135 93005 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→36.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 58 301 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172387
X-RAY DIFFRACTIONf_angle_d1.5833263
X-RAY DIFFRACTIONf_dihedral_angle_d11.951908
X-RAY DIFFRACTIONf_chiral_restr0.097350
X-RAY DIFFRACTIONf_plane_restr0.01419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.33921390.3332639X-RAY DIFFRACTION91
1.3148-1.33030.28371530.25312906X-RAY DIFFRACTION100
1.3303-1.34650.26111550.22162957X-RAY DIFFRACTION100
1.3465-1.36350.2211540.21372937X-RAY DIFFRACTION100
1.3635-1.38150.22161540.20072918X-RAY DIFFRACTION100
1.3815-1.40040.18791550.18652944X-RAY DIFFRACTION100
1.4004-1.42040.20011540.18522929X-RAY DIFFRACTION100
1.4204-1.44160.20531550.17252959X-RAY DIFFRACTION100
1.4416-1.46410.17791550.15522930X-RAY DIFFRACTION100
1.4641-1.48820.18971540.14462935X-RAY DIFFRACTION100
1.4882-1.51380.16791560.13552964X-RAY DIFFRACTION100
1.5138-1.54130.17191540.12572925X-RAY DIFFRACTION100
1.5413-1.5710.13581550.11922951X-RAY DIFFRACTION100
1.571-1.60310.14481550.10682933X-RAY DIFFRACTION100
1.6031-1.63790.12171560.10412959X-RAY DIFFRACTION100
1.6379-1.6760.12511530.10382923X-RAY DIFFRACTION100
1.676-1.71790.13961550.1012936X-RAY DIFFRACTION100
1.7179-1.76440.12821570.10752985X-RAY DIFFRACTION100
1.7644-1.81630.12821550.10792944X-RAY DIFFRACTION100
1.8163-1.87490.15541560.10772957X-RAY DIFFRACTION100
1.8749-1.94190.13321540.10832936X-RAY DIFFRACTION100
1.9419-2.01970.14751570.1142983X-RAY DIFFRACTION100
2.0197-2.11160.14051550.11362941X-RAY DIFFRACTION100
2.1116-2.22290.13571570.11552976X-RAY DIFFRACTION100
2.2229-2.36210.13821550.11832962X-RAY DIFFRACTION99
2.3621-2.54450.12971570.12352984X-RAY DIFFRACTION100
2.5445-2.80040.1641580.13372986X-RAY DIFFRACTION100
2.8004-3.20550.15581580.14263008X-RAY DIFFRACTION100
3.2055-4.03770.14521590.13223025X-RAY DIFFRACTION100
4.0377-36.1160.1821590.15753024X-RAY DIFFRACTION95

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