[English] 日本語
Yorodumi
- PDB-4tpi: THE REFINED 2.2-ANGSTROMS (0.22-NM) X-RAY CRYSTAL STRUCTURE OF TH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tpi
TitleTHE REFINED 2.2-ANGSTROMS (0.22-NM) X-RAY CRYSTAL STRUCTURE OF THE TERNARY COMPLEX FORMED BY BOVINE TRYPSINOGEN, VALINE-VALINE AND THE ARG15 ANALOGUE OF BOVINE PANCREATIC TRYPSIN INHIBITOR
Components
  • BOVINE PANCREATIC 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 / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / endopeptidase activity / protease binding / 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 / Few Secondary Structures ...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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
VALINE / Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsBode, W. / Walter, J.
Citation
Journal: Eur.J.Biochem. / Year: 1984
Title: The refined 2.2-A (0.22-nm) X-ray crystal structure of the ternary complex formed by bovine trypsinogen, valine-valine and the Arg15 analogue of bovine pancreatic trypsin inhibitor
Authors: Bode, W. / Walter, J. / Huber, R. / Wenzel, H.R. / Tschesche, H.
#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.
History
DepositionJun 11, 1985Processing site: BNL
Revision 1.0Nov 8, 1985Provider: 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 / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0357
Polymers30,5692
Non-polymers4665
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-47 kcal/mol
Surface area11880 Å2
MethodPISA
2
Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,14028
Polymers122,2748
Non-polymers1,86620
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 area17340 Å2
ΔGint-237 kcal/mol
Surface area40140 Å2
MethodPISA
3
Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules

Z: TRYPSINOGEN
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,07014
Polymers61,1374
Non-polymers93310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area6730 Å2
ΔGint-107 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.510, 85.450, 122.300
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: SEE REMARK 7. / 3: SEE REMARK 8.

-
Components

-
Protein , 2 types, 2 molecules ZI

#1: Protein TRYPSINOGEN


Mass: 24012.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein BOVINE PANCREATIC TRYPSIN INHIBITOR


Mass: 6555.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P00974

-
Non-polymers , 4 types, 160 molecules

#3: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsRESIDUE SER Z 195 HAS BEEN ALLOWED TO ACCESS INHIBITOR RESIDUES FREELY, I. E. IT IS NOT RESTRICTED ...RESIDUE SER Z 195 HAS BEEN ALLOWED TO ACCESS INHIBITOR RESIDUES FREELY, I. E. IT IS NOT RESTRICTED BY VAN DER WAALS REPULSIONS. IN THE DEPOSITED DATA THIS RESIDUE WAS IDENTIFIED AS *SIR* AND ATOM *OG* WAS IDENTIFIED AS *OI*.
Nonpolymer detailsTHE RESIDUES 1016 AND 1017 REPRESENT A DIPEPTIDE (VAL-VAL) BOUND TO THE ENZYME THE 229 AMINO ACIDS ...THE RESIDUES 1016 AND 1017 REPRESENT A DIPEPTIDE (VAL-VAL) BOUND TO THE ENZYME 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 VAL-VAL DIPEPTIDE IS GIVEN THE CHAIN INDICATOR S. A NULL (BLANK) CHAIN INDICATOR IS ASSIGNED TO ALL OTHER MOLECULES. THE NOMENCLATURE OF THE WATER MOLECULES IS THAT OF THE DEPOSITORS. TWO SOLVENT MOLECULES HAVE BEEN IDENTIFIED AS SULFATE ANIONS. THE CALCIUM SITE IS PARTIALLY OCCUPIED BY A CALCIUM ION. THE B-VALUES OF THE ATOMS OF THE PROTEIN ARE SEPARATELY AVERAGED OVER ALL MAIN CHAIN ATOMS (INCLUDING CB) AND THE REMAINING SIDE CHAIN ATOMS, RESPECTIVELY, OF EACH RESIDUE. THE B-VALUES OF THE SOLVENT MOLECULES ARE THE REFINED INDIVIDUAL VALUES.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5-1.7 Mmagnesium sulfate1drop
210 mg/mltrysinogen1drop
32 mg/ml[Arg15]PTI1drop

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.24 Å / Num. obs: 12422 / % possible obs: 63.8 % / Observed criterion σ(I): 1 / Num. measured all: 18470 / Rmerge(I) obs: 0.069

-
Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2.2→7 Å / Rfactor Rwork: 0.17
Details: THE SIDE CHAIN CONFORMATION OF VAL 1016 AS DESCRIBED IN THE JRNL REFERENCE ABOVE AND AS GIVEN ON THE ATOMS RECORDS BELOW IS ENERGETICALLY UNFAVORABLE. A MORE FAVORABLE CONFORMATION COULD BE ...Details: THE SIDE CHAIN CONFORMATION OF VAL 1016 AS DESCRIBED IN THE JRNL REFERENCE ABOVE AND AS GIVEN ON THE ATOMS RECORDS BELOW IS ENERGETICALLY UNFAVORABLE. A MORE FAVORABLE CONFORMATION COULD BE OBTAINED BY A 180 DEGREE SIDE CHAIN ROTATION ABOUT CHI 1 (VAL 1016 CA - CB). THE SIDE CHAIN CONFORMATION OF VAL S 16 AS DESCRIBED IN THE JRNL REFERENCE ABOVE AND AS GIVEN ON THE ATOMS RECORDS BELOW IS ENERGETICALLY UNFAVORABLE. A MORE FAVORABLE CONFORMATION COULD BE OBTAINED BY A 180 DEGREE SIDE CHAIN ROTATION ABOUT CHI 1 (VAL S 16 CA - CB).
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 26 155 2266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.37
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2.24 Å / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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