[English] 日本語
Yorodumi
- PDB-5pti: STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR. RESULTS OF JOIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5pti
TitleSTRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR. RESULTS OF JOINT NEUTRON AND X-RAY REFINEMENT OF CRYSTAL FORM II
ComponentsTRYPSIN INHIBITOR
KeywordsHydrolase Inhibitor / PROTEINASE INHIBITOR (TRYPSIN)
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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
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
Similarity search - Domain/homology
DEUTERATED WATER / PHOSPHATE ION / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / Resolution: 1 Å
AuthorsWlodawer, A. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1984
Title: Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II
Authors: Wlodawer, A. / Walter, J. / Huber, R. / Sjolin, L.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Comparison of Two Highly Refined Structures of Bovine Pancreatic Trypsin Inhibitor
Authors: Wlodawer, A. / Deisenhofer, J. / Huber, R.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Pancreatic Trypsin Inhibitor. A New Crystal Form and its Analysis
Authors: Walter, J. / Huber, R.
History
DepositionOct 5, 1984Processing site: BNL
Revision 1.0Oct 29, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Data collection
Revision 1.4Oct 24, 2018Group: Data collection / Other / Structure summary / Category: pdbx_database_status / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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
A: TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6233
Polymers6,5281
Non-polymers952
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.100, 23.400, 28.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE ATOMS IN THE SIDE CHAIN OF RESIDUES GLU 7 AND MET 52 WERE FOUND TO OCCUPY TWO MAJOR SITES. THESE ATOMS ARE DENOTED WITH ALTERNATE LOCATION INDICATORS *A* AND *B*.
2: HETATM UNK 324 IS PROBABLY A POTASSIUM ION IN A PARTIALLY OCCUPIED SITE.

-
Components

#1: Protein TRYPSIN INHIBITOR


Mass: 6527.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00974
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY
Nonpolymer detailsHETATM UNX 324 IS PROBABLY A POTASSIUM ION IN A PARTIALLY OCCUPIED SITE.

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal grow
*PLUS
pH: 10 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
20.1 MK-Na phosphate1drop

-
Data collection

Reflection
*PLUS
Highest resolution: 0.94 Å / Lowest resolution: 9999 Å / Num. all: 33612 / Num. obs: 26499 / % possible obs: 76.4 % / Num. measured all: 41385 / Rmerge(I) obs: 0.049

-
Processing

RefinementHighest resolution: 1 Å
Refinement stepCycle: LAST / Highest resolution: 1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 6 63 523
Refinement
*PLUS
Highest resolution: 1 Å / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_bond_d / Dev ideal: 0.02

+
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