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- PDB-4pti: THE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TR... -

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Entry
Database: PDB / ID: 4pti
TitleTHE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TRYPSIN, TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS
ComponentsTRYPSIN INHIBITOR
KeywordsPROTEINASE INHIBITOR (TRYPSIN)
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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
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
Similarity search - Domain/homology
Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsHuber, R. / Kukla, D. / Ruehlmann, A. / Epp, O. / Formanek, H. / Deisenhofer, J. / Steigemann, W.
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: 1987
Title: Comparison of Two Highly Refined Structures of Bovine Pancreatic Trypsin Inhibitor
Authors: Wlodawer, A. / Deisenhofer, J. / Huber, R.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1975
Title: Crystallographic Refinement of the Structure of Bovine Pancreatic Trypsin Inhibitor at 1.5 Angstroms Resolution
Authors: Deisenhofer, J. / Steigemann, W.
#3: Journal: Bayer Symp. / Year: 1974
Title: The Model of the Basic Pancreatic Trypsin Inhibitor Refined at 1.5 Angstroms Resolution
Authors: Deisenhofer, J. / Steigemann, W.
#4: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Pancreatic Trypsin Inhibitor (Kunitz). Part I. Structure and Function
Authors: Huber, R. / Kukla, D. / Ruehlmann, A. / Steigemann, W.
#5: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Pancreatic Trypsin Inhibitor (Kunitz). Part II. Complexes with Proteinases
Authors: Ruehlmann, A. / Schramm, H.J. / Kukla, D. / Huber, R.
#6: Journal: Naturwissenschaften / Year: 1970
Title: The Basic Trypsin Inhibitor of Bovine Pancreas. I. Structure Analysis and Conformation of the Polypeptide Chain
Authors: Huber, R. / Kukla, D. / Ruehlmann, A. / Epp, O. / Formanek, H.
#7: Journal: Atlas of Protein Sequence and Structure,Supplement 1
Year: 1973
History
DepositionSep 27, 1982Processing site: BNL
SupersessionJan 18, 1983ID: 3PTI
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 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)6,5281
Polymers6,5281
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.100, 22.900, 48.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPSIN INHIBITOR


Mass: 6527.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.01 %
Crystal grow
*PLUS
Method: unknown

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Processing

RefinementResolution: 1.5→7 Å / Rfactor Rwork: 0.162
Refinement stepCycle: LAST / Resolution: 1.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 0 60 514

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