[English] 日本語
Yorodumi
- PDB-2tpi: ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2tpi
TitleON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABELLING AND LOW-TEMPERATURE CRYSTALLOGRAPHY
Components
  • 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 / 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
: / ISOLEUCINE / VALINE / Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsWalter, J. / Steigemann, W. / Singh, T.P. / Bartunik, H. / Bode, W. / Huber, R.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: On the Disordered Activation Domain in Trypsinogen. Chemical Labelling and Low-Temperature Crystallography
Authors: Walter, J. / Steigemann, W. / Singh, T.P. / Bartunik, H. / 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, W. / 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.
History
DepositionOct 26, 1981Processing site: BNL
Revision 1.0Mar 4, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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 1.4Nov 13, 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
Z: TRYPSINOGEN
I: TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9895
Polymers30,5412
Non-polymers4493
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-37 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.670, 84.160, 122.890
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.
2: IN THE DISULFIDE CYS 191 - CYS 220 A MERCURY ATOM IS COVALENTLY BOUND BETWEEN THE TWO SULFUR ATOMS. IT ADOPTS SEVERAL POSITIONS AS DO THE ADJACENT ATOMS. A SPECIAL MERCURY-CYSTINE GROUP WAS ...2: IN THE DISULFIDE CYS 191 - CYS 220 A MERCURY ATOM IS COVALENTLY BOUND BETWEEN THE TWO SULFUR ATOMS. IT ADOPTS SEVERAL POSITIONS AS DO THE ADJACENT ATOMS. A SPECIAL MERCURY-CYSTINE GROUP WAS CONSTRUCTED WHICH HAD THREE INDEPENDENT POSITIONS FOR THE CB, SG AND HG ATOMS.

-
Components

-
Protein , 2 types, 2 molecules ZI

#1: Protein TRYPSINOGEN


Mass: 24012.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P00760, trypsin
#2: Protein TRYPSIN INHIBITOR / Basic protease inhibitor / Aprotinin


Mass: 6527.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00974

-
Non-polymers , 4 types, 142 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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTHE RESIDUES 1016 AND 1017 REPRESENT A DIPEPTIDE (ILE-VAL) BOUND TO THE ENZYME THE N-TERMINUS OF ...THE RESIDUES 1016 AND 1017 REPRESENT A DIPEPTIDE (ILE-VAL) BOUND TO THE ENZYME THE N-TERMINUS OF THE ZYMOGEN COMPONENT IS ORDERED ONLY FROM GLY 19 ONWARDS. THIS ENTRY CONTAINS NO COORDINATES FOR VAL 10 THROUGH GLY 18. ATOMS 1 THROUGH 17 BELONG TO THE ILE-VAL-DIPEPTIDE. IN THE INHIBITOR COMPONENT ARG 1 AND ALA 58 ARE DISORDERED AND NO COORDINATES ARE PRESENTED FOR THEM.
Has protein modificationY
Nonpolymer detailsIN THE DISULFIDE CYS 191 - CYS 220 A MERCURY ATOM IS COVALENTLY BOUND BETWEEN THE TWO SULFUR ATOMS. ...IN THE DISULFIDE CYS 191 - CYS 220 A MERCURY ATOM IS COVALENTLY BOUND BETWEEN THE TWO SULFUR ATOMS. IT ADOPTS SEVERAL POSITIONS AS DO THE ADJACENT ATOMS. A SPECIAL MERCURY-CYSTINE GROUP WAS CONSTRUCTED WHICH HAD THREE INDEPENDENT POSITIONS FOR THE CB, SG AND HG ATOMS.
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, 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 WATER MOLECULES.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
33.5 mg/mlIle-Val dipeptide1drop
41.5 M1dropMgSO4
51.5 M1reservoirMgSO4
2pancreatic trypsin inhibitor1dropequimolar amount

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

RefinementResolution: 2.1→6.5 Å / Rfactor Rwork: 0.2
Details: IN THE DISULFIDE CYS 191 - CYS 220 A MERCURY ATOM IS COVALENTLY BOUND BETWEEN THE TWO SULFUR ATOMS. IT ADOPTS SEVERAL POSITIONS AS DO THE ADJACENT ATOMS. A SPECIAL MERCURY-CYSTINE GROUP WAS ...Details: IN THE DISULFIDE CYS 191 - CYS 220 A MERCURY ATOM IS COVALENTLY BOUND BETWEEN THE TWO SULFUR ATOMS. IT ADOPTS SEVERAL POSITIONS AS DO THE ADJACENT ATOMS. A SPECIAL MERCURY-CYSTINE GROUP WAS CONSTRUCTED WHICH HAD THREE INDEPENDENT POSITIONS FOR THE CB, SG AND HG ATOMS.
Refinement stepCycle: LAST / Resolution: 2.1→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 19 139 2214
Refinement
*PLUS
Num. reflection obs: 14327 / Highest resolution: 2.1 Å / Lowest resolution: 6.5 Å / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21 Å2

+
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