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- PDB-3tpi: THE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TR... -

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Basic information

Entry
Database: PDB / ID: 3tpi
TitleTHE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TRYPSIN, TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS
Components
  • BOVINE PANCREATIC TRYPSIN INHIBITOR
  • TRYPSINOGEN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / COMPLEX (PROTEINASE-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 / 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
ISOLEUCINE / VALINE / Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHuber, R. / Bode, W. / Deisenhofer, J. / Schwager, P.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors
Authors: Marquart, M. / Walter, J. / Deisenhofer, J. / Bode, W. / Huber, R.
#1: Journal: J.Mol.Biol. / Year: 1979
Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. II. The Binding of the Pancreatic Trypsin Inhibitor and of Isoleucine-Valine and of Sequentially ...Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. II. The Binding of the Pancreatic Trypsin Inhibitor and of Isoleucine-Valine and of Sequentially Related Peptides to Trypsinogen and to P-Guanidinobenzoate-Trypsinogen
Authors: Bode, W.
#2: Journal: J.Mol.Biol. / Year: 1978
Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. The Refined Crystal Structures of the Bovine Trypsinogen-Pancreatic Trypsin Inhibitor Complex and of ...Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. The Refined Crystal Structures of the Bovine Trypsinogen-Pancreatic Trypsin Inhibitor Complex and of its Ternary Complex with Ile-Val at 1.9 Angstroms Resolution
Authors: Bode, W. / Schwager, P. / Huber, R.
#3: Journal: Acc.Chem.Res. / Year: 1978
Title: Structural Basis of the Activation and Action of Trypsin
Authors: Huber, R. / Bode, W.
#4: Journal: Biophys.Struct.Mech. / Year: 1975
Title: The Structure of the Complex Formed by Bovine Trypsin and Bovine Pancreatic Trypsin Inhibitor. III. Structure of the Anhydro-Trypsin-Inhibitor Complex
Authors: Huber, R. / Bode, W. / Kukla, D. / Kohl, U. / Ryan, C.A.
#5: Journal: J.Mol.Biol. / Year: 1974
Title: Structure of the Complex Formed by Bovine Trypsin and Bovine Pancreatic Trypsin Inhibitor. II. Crystallographic Refinement at 1.9 Angstroms Resolution
Authors: Huber, R. / Kukla, D. / Bode, W. / Schwager, P. / Bartels, K. / Deisenhofer, J. / Steigemann, W.
#6: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
Authors: Dayhoff, M.O.
#7: Journal: Atlas of Protein Sequence and Structure,Supplement 1
Year: 1973
Authors: Dayhoff, M.O.
History
DepositionSep 27, 1982Processing site: BNL
SupersessionJan 18, 1983ID: 1TPI
Revision 1.0Jan 18, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2012Group: Derived calculations
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0217
Polymers30,5412
Non-polymers4815
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-45 kcal/mol
Surface area11890 Å2
MethodPISA
2
Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,08428
Polymers122,1628
Non-polymers1,92220
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area14700 Å2
ΔGint-230 kcal/mol
Surface area40340 Å2
MethodPISA
3
Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,04214
Polymers61,0814
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area5430 Å2
ΔGint-104 kcal/mol
Surface area22090 Å2
MethodPISA
4
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0217
Polymers30,5412
Non-polymers4815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area1280 Å2
ΔGint-46 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.500, 84.400, 122.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: SEE REMARK 4.
Components on special symmetry positions
IDModelComponents
11I-588-

HOH

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Components

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Protein , 2 types, 2 molecules ZI

#1: Protein TRYPSINOGEN


Mass: 24012.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein BOVINE PANCREATIC TRYPSIN INHIBITOR


Mass: 6527.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P00974

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Non-polymers , 5 types, 157 molecules

#3: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE RESIDUES 1016 AND 1017 REPRESENT A DIPEPTIDE (ILE-VAL) BOUND TO THE ENZYME THE 229 AMINO ACIDS ...THE RESIDUES 1016 AND 1017 REPRESENT A DIPEPTIDE (ILE-VAL) BOUND TO THE ENZYME THE 229 AMINO ACIDS OF TRYPSINOGEN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS CHYMOTRYPSINOGEN. IN THIS COMPLEX THE ZYMOGEN IS GIVEN THE CHAIN INDICATOR Z, THE INHIBITOR IS GIVEN THE CHAIN INDICATOR I, AND THE ILE-VAL DIPEPTIDE IS GIVEN THE CHAIN INDICATOR S. A NULL (BLANK) CHAIN INDICATOR IS ASSIGNED TO THE CALCIUM AND TO THE WATER MOLECULES. THE NOMENCLATURE OF THE WATER MOLECULES IS THAT OF THE DEPOSITORS.

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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: 61.32 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementResolution: 1.9→6.8 Å / Rfactor Rwork: 0.193
Refinement stepCycle: LAST / Resolution: 1.9→6.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 27 152 2262

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