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- PDB-1tgs: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN PANCREATIC SEC... -

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Basic information

Entry
Database: PDB / ID: 1tgs
TitleTHREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN PANCREATIC SECRETORY INHIBITOR (KAZAL TYPE) AND TRYPSINOGEN AT 1.8 ANGSTROMS RESOLUTION. STRUCTURE SOLUTION, CRYSTALLOGRAPHIC REFINEMENT AND PRELIMINARY STRUCTURAL INTERPRETATION
Components
  • PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE)
  • TRYPSINOGEN
KeywordsCOMPLEX (PROTEINASE/INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / : ...Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / : / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serine protease 1 / Serine protease inhibitor Kazal-type 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBolognesi, M. / Gatti, G. / Menegatti, E. / Guarneri, M. / Marquart, M. / Papamokos, E. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Three-dimensional structure of the complex between pancreatic secretory trypsin inhibitor (Kazal type) and trypsinogen at 1.8 A resolution. Structure solution, crystallographic refinement and ...Title: Three-dimensional structure of the complex between pancreatic secretory trypsin inhibitor (Kazal type) and trypsinogen at 1.8 A resolution. Structure solution, crystallographic refinement and preliminary structural interpretation.
Authors: Bolognesi, M. / Gatti, G. / Menagatti, E. / Guarneri, M. / Marquart, M. / Papamokos, E. / Huber, R.
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: 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.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
Revision 1.4Nov 6, 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

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Assembly

Deposited unit
Z: TRYPSINOGEN
I: PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1784
Polymers30,0422
Non-polymers1362
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-34 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.100, 75.500, 66.900
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 TRYPSINOGEN


Mass: 24012.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760
#2: Protein PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE)


Mass: 6028.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00998
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 229 AMINO ACIDS OF TRYPSINOGEN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS ...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 AND THE INHIBITOR IS GIVEN THE CHAIN INDICATOR I. A NULL (BLANK) CHAIN INDICATOR IS ASSIGNED TO THE SULFATE, 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal grow
*PLUS
Method: other / Details: Bolognesi, M., (1981) J. Mol. Biol., 145, 603.

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 26341 / % possible obs: 84 % / Rmerge(I) obs: 0.084

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Processing

RefinementResolution: 1.8→7 Å / Rfactor Rwork: 0.186
Refinement stepCycle: LAST / Resolution: 1.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 6 162 2230
Refinement
*PLUS
Num. reflection obs: 26341 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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