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- PDB-1cbw: BOVINE CHYMOTRYPSIN COMPLEXED TO BPTI -

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Basic information

Entry
Database: PDB / ID: 1cbw
TitleBOVINE CHYMOTRYPSIN COMPLEXED TO BPTI
Components
  • (BOVINE CHYMOTRYPSIN) x 3
  • BPTI
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / SERINE PROTEASE / INHIBITOR / PROTEASE-SUBSTRATE INTERACTIONS / COMPLEX (SERINE PROTEASE-INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


chymotrypsin / 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 / serpin family protein binding ...chymotrypsin / 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 / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
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
Chymotrypsinogen A / Chymotrypsinogen B / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHynes, T.R. / Scheidig, A.J. / Kossiakoff, A.A.
Citation
Journal: Protein Sci. / Year: 1997
Title: Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): ...Title: Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities.
Authors: Scheidig, A.J. / Hynes, T.R. / Pelletier, L.A. / Wells, J.A. / Kossiakoff, A.A.
#1: Journal: Biochemistry / Year: 1990
Title: X-Ray Crystal Structure of the Protease Inhibitor Domain of Alzheimer'S Amyloid Beta-Protein Precursor
Authors: Hynes, T.R. / Randal, M. / Kennedy, L.A. / Eigenbrot, C. / Kossiakoff, A.A.
History
DepositionDec 22, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status ...diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: BOVINE CHYMOTRYPSIN
B: BOVINE CHYMOTRYPSIN
C: BOVINE CHYMOTRYPSIN
D: BPTI
F: BOVINE CHYMOTRYPSIN
G: BOVINE CHYMOTRYPSIN
H: BOVINE CHYMOTRYPSIN
I: BPTI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,77210
Polymers63,5808
Non-polymers1922
Water2,846158
1
A: BOVINE CHYMOTRYPSIN
B: BOVINE CHYMOTRYPSIN
C: BOVINE CHYMOTRYPSIN
D: BPTI


Theoretical massNumber of molelcules
Total (without water)31,7904
Polymers31,7904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-67 kcal/mol
Surface area12550 Å2
MethodPISA
2
F: BOVINE CHYMOTRYPSIN
G: BOVINE CHYMOTRYPSIN
H: BOVINE CHYMOTRYPSIN
I: BPTI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9826
Polymers31,7904
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-95 kcal/mol
Surface area12540 Å2
MethodPISA
3
F: BOVINE CHYMOTRYPSIN
G: BOVINE CHYMOTRYPSIN
H: BOVINE CHYMOTRYPSIN
I: BPTI
hetero molecules

A: BOVINE CHYMOTRYPSIN
B: BOVINE CHYMOTRYPSIN
C: BOVINE CHYMOTRYPSIN
D: BPTI


Theoretical massNumber of molelcules
Total (without water)63,77210
Polymers63,5808
Non-polymers1922
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
Buried area19860 Å2
ΔGint-176 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.600, 101.600, 205.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.35757, 0.933886, -0.000358), (0.933674, 0.35748, -0.021455), (-0.019909, -0.008006, -0.99977)
Vector: 0.7151, -0.3038, 5.2355)
DetailsTHE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ZYMOGEN OF THIS ENZYME BY EXCISION OF RESIDUES 14 - 15 AND 147 - 148. THE TWO INDEPENDENT CHYMOTRYPSIN MOLECULES IN THE ASYMMETRIC UNIT HAVE BEEN ASSIGNED CHAIN IDENTIFIERS A, B, C, AND F, G, H. THE TRANSFORMATION SUPPLIED IN THE *MTRIX* RECORDS BELOW WILL GENERATE APPROXIMATE COORDINATES FOR CHAINS F, G, H WHEN APPLIED TO CHAINS A, B, C.

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Components

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Protein/peptide , 1 types, 2 molecules AF

#1: Protein/peptide BOVINE CHYMOTRYPSIN


Mass: 1253.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P00767, UniProt: P00766*PLUS, chymotrypsin

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Protein , 3 types, 6 molecules BGCHDI

#2: Protein BOVINE CHYMOTRYPSIN


Mass: 13934.556 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein BOVINE CHYMOTRYPSIN


Mass: 10074.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#4: Protein BPTI / BASIC PANCREATIC TRYPSIN INHIBITOR


Mass: 6527.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00974

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Non-polymers , 2 types, 160 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.82 Å3/Da / Density % sol: 74.5 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlcomplex1drop
20.5 %(v/v)MPD1drop
350 %(v/v)ammonium sulfate1drop
480 mMTris-HCl1drop
550 %(v/v)ammonium sulfate1reservoir
680 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 1, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32244 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.0872 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 1.5 / % possible all: 55
Reflection shell
*PLUS
% possible obs: 55 %

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Processing

Software
NameVersionClassification
MADNESdata collection
PROCORdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
PROCORdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTTY 5CHA + 2PTC

5cha

2ptc


Resolution: 2.6→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: FOR THE LAST TWO RUNS / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 -10 %RANDOM
Rwork0.192 ---
obs0.192 32244 89 %-
Displacement parametersBiso mean: 36.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 10 158 4590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.944
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.47
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.627
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.376 261 7.2 %
Rwork0.311 2240 -
obs--69.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.SO4TOP.SO4
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.47
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.627

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