[English] 日本語
Yorodumi
- PDB-2ptc: THE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ptc
TitleTHE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TRYPSIN, TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS
Components
  • BETA-TRYPSIN
  • TRYPSIN INHIBITOR
KeywordsCOMPLEX (PROTEINASE/INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) / COMPLEX (PROTEINASE-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
Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHuber, R. / Deisenhofer, J.
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: 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.
#2: 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.
#3: Journal: FEBS Lett. / Year: 1975
Title: The Single Calcium-Binding Site of Crystalline Bovine Beta-Trypsin
Authors: Bode, W. / Schwager, P.
#4: Journal: Bayer Symp. / Year: 1974
Title: Structure of the Complex Formed by Bovine Trypsin and Bovine Pancreatic Trypsin Inhibitor. Refinement of the Crystal Structure Analysis
Authors: Huber, R. / Kukla, D. / Steigemann, W. / Deisenhofer, J. / Jones, 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: J.Mol.Biol. / Year: 1973
Title: Structure of the Complex Formed by Bovine Trypsin and Bovine Pancreatic Trypsin Inhibitor. Crystal Structure Determination and Stereochemistry of the Contact Region
Authors: Ruehlmann, A. / Kukla, D. / Schwager, P. / Bartels, K. / Huber, R.
#7: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
#8: Journal: Atlas of Protein Sequence and Structure,Supplement 1
Year: 1973
History
DepositionSep 27, 1982Processing site: BNL
SupersessionJan 18, 1983ID: 1PTC
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 ...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 / pdbx_struct_special_symmetry / 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: BETA-TRYPSIN
I: TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8923
Polymers29,8522
Non-polymers401
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-19 kcal/mol
Surface area11660 Å2
MethodPISA
2
E: BETA-TRYPSIN
I: TRYPSIN INHIBITOR
hetero molecules

E: BETA-TRYPSIN
I: TRYPSIN INHIBITOR
hetero molecules

E: BETA-TRYPSIN
I: TRYPSIN INHIBITOR
hetero molecules

E: BETA-TRYPSIN
I: TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,56812
Polymers119,4078
Non-polymers1604
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 area12850 Å2
ΔGint-100 kcal/mol
Surface area39860 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-423-

HOH

-
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 (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein TRYPSIN INHIBITOR


Mass: 6527.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P00974
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 157 / 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 ENZYME IS GIVEN THE CHAIN INDICATOR E AND THE INHIBITOR IS GIVEN THE CHAIN INDICATOR I. 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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal grow
*PLUS
Method: unknown

-
Processing

RefinementResolution: 1.9→6.8 Å / Rfactor Rwork: 0.187
Refinement stepCycle: LAST / Resolution: 1.9→6.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 1 157 2241

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more