[English] 日本語
Yorodumi
- PDB-2gch: REFINED CRYSTAL STRUCTURE OF GAMMA-CHYMOTRYPSIN AT 1.9 ANGSTROMS ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gch
TitleREFINED CRYSTAL STRUCTURE OF GAMMA-CHYMOTRYPSIN AT 1.9 ANGSTROMS RESOLUTION
Components(GAMMA-CHYMOTRYPSIN A) x 3
KeywordsHYDROLASE (SERINE PROTEINASE)
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
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 ...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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsCohen, G.H. / Davies, D.R. / Silverton, E.W.
Citation
Journal: J.Mol.Biol. / Year: 1981
Title: Refined crystal structure of gamma-chymotrypsin at 1.9 A resolution. Comparison with other pancreatic serine proteases.
Authors: Cohen, G.H. / Silverton, E.W. / Davies, D.R.
#1: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: The Stereochemistry of Substrate Binding to Chymotrypsin A Gamma
Authors: Segal, D.M. / Cohen, G.H. / Davies, D.R. / Powers, J.C. / Wilcox, P.E.
#2: Journal: Biochemistry / Year: 1971
Title: Substrate Binding Site in Chymotrypsin A Gamma, Crystallographic Study Using Peptide Chloromethyl Ketones as Site-Specific Inhibitors
Authors: Segal, D.M. / Powers, J.C. / Cohen, G.H. / Davies, D.R. / Wilcox, P.E.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1970
Title: The Relation between Gamma-and Alpha-Chymotrypsin, II.Direct Comparison of the Electron Densities at 5.5 Angstroms Resolution
Authors: Cohen, G.H. / Matthews, B.W. / Davies, D.R.
#4: Journal: J.Mol.Biol. / Year: 1969
Title: Structure of Gamma-Chymotrypsin at 5.5 Angstroms Resolution
Authors: Cohen, G.H. / Silverton, E.W. / Matthews, B.W. / Braxton, H. / Davies, D.R.
#5: Journal: J.Mol.Biol. / Year: 1968
Title: Relation between Gamma-and Alpha-Chymotrypsin
Authors: Matthews, B.W. / Cohen, G.H. / Silverton, E.W. / Braxton, H. / Davies, D.R.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1964
Title: The Isomorphous Heavy-Atom Substitution at the Active Site of Gamma Chymotrypsin
Authors: Sigler, P.B. / Skinner, H.C.W. / Coulter, C.L. / Kallos, J. / Braxton, H. / Davies, D.R.
#7: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#8: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMay 21, 1980Processing site: BNL
SupersessionJul 9, 1980ID: 1GCH
Revision 1.0Jul 9, 1980Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jun 5, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A


Theoretical massNumber of molelcules
Total (without water)25,2633
Polymers25,2633
Non-polymers00
Water2,720151
1
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A

E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A


Theoretical massNumber of molelcules
Total (without water)50,5256
Polymers50,5256
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-57 kcal/mol
Surface area10050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.600, 69.600, 97.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11F-229-

HOH

-
Components

#1: Protein/peptide GAMMA-CHYMOTRYPSIN A


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein GAMMA-CHYMOTRYPSIN A


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein GAMMA-CHYMOTRYPSIN A


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal grow
*PLUS
pH: 5.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
250 %satammonium sulfate11
1protein1125mg

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 19650 / Num. obs: 15395

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→7 Å /
RfactorNum. reflection
Rwork0.181 -
obs-14992
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 151 1889
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_plane_restr0.0120.02
X-RAY DIFFRACTIONo_chiral_restr0.2080.15

+
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