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- PDB-2ra3: Human cationic trypsin complexed with bovine pancreatic trypsin i... -

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Basic information

Entry
Database: PDB / ID: 2ra3
TitleHuman cationic trypsin complexed with bovine pancreatic trypsin inhibitor (BPTI)
Components
  • Pancreatic trypsin inhibitor
  • Trypsin-1
Keywordshydrolase/hydrolase inhibitor / Human cationic trypsin / Serine protease / Bovine pancreatic trypsin inhibitor / BPTI / Calcium / Digestion / Disease mutation / Hydrolase / Metal-binding / Secreted / Sulfation / Zymogen / Pharmaceutical / Protease inhibitor / Serine protease inhibitor / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / Developmental Lineage of Pancreatic Acinar Cells / zymogen binding / molecular function inhibitor activity / Activation of Matrix Metalloproteinases ...Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / Developmental Lineage of Pancreatic Acinar Cells / zymogen binding / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / negative regulation of thrombin-activated receptor signaling pathway / extracellular matrix disassembly / trypsin / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / : / blood microparticle / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / 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 / 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
Pancreatic trypsin inhibitor / Serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsSalameh, M.A. / Soares, A.S. / Radisky, E.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Basis for Accelerated Cleavage of Bovine Pancreatic Trypsin Inhibitor (BPTI) by Human Mesotrypsin.
Authors: Salameh, M.A. / Soares, A.S. / Hockla, A. / Radisky, E.S.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin-1
B: Trypsin-1
I: Pancreatic trypsin inhibitor
C: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,64530
Polymers61,2594
Non-polymers2,38626
Water11,584643
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Trypsin-1
C: Pancreatic trypsin inhibitor
hetero molecules

A: Trypsin-1
C: Pancreatic trypsin inhibitor
hetero molecules

B: Trypsin-1
I: Pancreatic trypsin inhibitor
hetero molecules

B: Trypsin-1
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,29060
Polymers122,5198
Non-polymers4,77152
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation6_544-x+1/2,-y-1/2,z-1/21
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area23350 Å2
ΔGint-746.2 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.183, 186.546, 90.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-340-

HOH

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Components

#1: Protein Trypsin-1 / Trypsin I / Cationic trypsinogen / Serine protease 1


Mass: 24102.154 Da / Num. of mol.: 2 / Mutation: R117H, S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P07477, trypsin
#2: Protein Pancreatic trypsin inhibitor / Basic protease inhibitor / BPI / BPTI / Aprotinin


Mass: 6527.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Strain: A1153 / References: UniProt: P00974
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris hydrochloride pH 8.5, 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.46→26.144 Å / Num. obs: 115118 / % possible obs: 87.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 17.335 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 19.5
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.465 / % possible all: 46.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1TRN and 2PTC

1trn

2ptc


Resolution: 1.46→26.13 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 11506 -Random
Rwork0.153 ---
obs0.1539 115064 86.8 %-
all-115064 --
Displacement parametersBiso mean: 16.36 Å2
Refinement stepCycle: LAST / Resolution: 1.46→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 127 665 5248
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_bond_d_na
X-RAY DIFFRACTIONf_bond_d_prot
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_angle_d_na
X-RAY DIFFRACTIONf_angle_d_prot
X-RAY DIFFRACTIONf_angle_deg0.793
X-RAY DIFFRACTIONf_angle_deg_na
X-RAY DIFFRACTIONf_angle_deg_prot
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d_na
X-RAY DIFFRACTIONf_dihedral_angle_d_prot
X-RAY DIFFRACTIONf_improper_angle_d
X-RAY DIFFRACTIONf_improper_angle_d_na
X-RAY DIFFRACTIONf_improper_angle_d_prot
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it

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