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- PDB-1tpp: THE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TR... -

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Basic information

Entry
Database: PDB / ID: 1tpp
TitleTHE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TRYPSIN, TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / 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 ...: / 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
Chem-APA / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsWalter, J. / Bode, W. / Huber, R.
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: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1983
Title: The X-Ray Crystal Structure Analysis of the Refined Complex Formed by Bovine Trypsin and P-Amidinophenylpyruvate at 1.4 Angstroms Resolution
Authors: Walter, J. / Bode, W.
#2: Journal: Miami Winter Symp. / Year: 1976
Title: Structural Studies on the Pancreatic Trypsin Inhibitor-Trypsin Complex and its Free Components. Structure and Function Relationships in Serine Protease Inhibition and Catalysis
Authors: Bode, W. / Schwager, P. / Huber, R.
#3: Journal: J.Mol.Biol. / Year: 1975
Title: The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 Angstroms Resolution. I. Crystallization, Data Collection and Application of Patterson Search Techniques
Authors: Fehlhammer, H. / Bode, W.
#4: Journal: J.Mol.Biol. / Year: 1975
Title: The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 Angstroms Resolution. II. Crystallographic Refinement, Calcium Binding Site, Benzamidine Binding Site and Active Site at Ph 7.0
Authors: Bode, W. / Schwager, P.
#5: Journal: FEBS Lett. / Year: 1975
Title: The Single Calcium-Binding Site of Crystalline Bovine Beta-Trypsin
Authors: Bode, W. / Schwager, P.
#6: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionSep 27, 1982Processing site: BNL
Revision 1.0Jan 18, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jun 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6694
Polymers23,3241
Non-polymers3443
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.900, 58.500, 67.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEE REMARK 4.

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Components

#1: Protein BETA-TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-APA / (2S)-3-(4-carbamimidoylphenyl)-2-hydroxypropanoic acid


Mass: 208.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE C2 ATOM OF P-AMIDINO-PHENYL-PYRUVATE APA1A IS COVALENTLY CONNECTED TO SER195A SIDE CHAIN ATOM ...THE C2 ATOM OF P-AMIDINO-PHENYL-PYRUVATE APA1A IS COVALENTLY CONNECTED TO SER195A SIDE CHAIN ATOM OG, FORMING HEMIKETAL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.28 %
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: 1.4→6.5 Å / Rfactor Rwork: 0.191
Refinement stepCycle: LAST / Resolution: 1.4→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 21 93 1743

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