[English] 日本語
Yorodumi
- PDB-1cho: CRYSTAL AND MOLECULAR STRUCTURES OF THE COMPLEX OF ALPHA-*CHYMOTR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cho
TitleCRYSTAL AND MOLECULAR STRUCTURES OF THE COMPLEX OF ALPHA-*CHYMOTRYPSIN WITH ITS INHIBITOR TURKEY OVOMUCOID THIRD DOMAIN AT 1.8 ANGSTROMS RESOLUTION
Components
  • (ALPHA-CHYMOTRYPSIN A) x 3
  • TURKEY OVOMUCOID THIRD DOMAIN (OMTKY3)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE-INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


chymotrypsin / molecular function inhibitor activity / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / : / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...Proteinase inhibitor I1, Kazal-type, metazoa / : / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chymotrypsinogen A / Ovomucoid
Similarity search - Component
Biological speciesBos taurus (cattle)
Meleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFujinaga, M. / Sielecki, A.R. / Read, R.J. / Ardelt, W. / Laskowskijunior, M. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 1987
Title: Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution.
Authors: Fujinaga, M. / Sielecki, A.R. / Read, R.J. / Ardelt, W. / Laskowski Jr., M. / James, M.N.
History
DepositionMar 4, 1988Processing site: BNL
Revision 1.0Jul 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: ALPHA-CHYMOTRYPSIN A
F: ALPHA-CHYMOTRYPSIN A
G: ALPHA-CHYMOTRYPSIN A
I: TURKEY OVOMUCOID THIRD DOMAIN (OMTKY3)


Theoretical massNumber of molelcules
Total (without water)31,2894
Polymers31,2894
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-71 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.920, 54.520, 57.180
Angle α, β, γ (deg.)90.00, 103.90, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: LYS E 36 - POOR DENSITY FOR ALL ATOMS BEYOND CG.
2: GLY E 74 THROUGH SER E 77 - POOR DENSITY FOR BOTH SIDE CHAIN AND MAIN CHAIN ATOMS. EXTERNAL LOOP.
3: LYS E 84 - POOR DENSITY FOR ALL ATOMS BEYOND CD. / 4: LYS E 87 - POOR DENSITY FOR ALL ATOMS BEYOND CG. / 5: LYS E 93 - POOR DENSITY FOR ALL ATOMS BEYOND CG. / 6: LEU E 97 - POOR DENSITY FOR ALL ATOMS BEYOND CB.
7: ALA E 149 AND ASN E 150 - N TERMINUS OF CHAIN 3 OF CHYMOTRYPSIN. VERY WEAK DENSITY FOR BOTH RESIDUES.
8: ARG E 154 - POOR DENSITY FOR CZ, NH1, NH2. / 9: LYS E 203 - POOR DENSITY FOR NZ. / 10: VAL I 4 - POOR DENSITY FOR MAIN CHAIN NITROGEN. / 11: LYS I 29 - POOR DENSITY FOR ATOMS BEYOND CD. / 12: LYS I 34 - AMBIGUOUS POSITIONING OF CD, CE, NZ.
13: LYS I 55 - POOR DENSITY FOR END OF SIDE CHAIN BEYOND CG.
14: RESIDUE PRO I 12 IS A CIS PROLINE.

-
Components

#1: Protein/peptide ALPHA-CHYMOTRYPSIN A


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


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


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Protein TURKEY OVOMUCOID THIRD DOMAIN (OMTKY3)


Mass: 6026.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P68390
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Compound details1CHO THE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE 1CHO POLYPEPTIDE CHAINS WHICH ARE ...1CHO THE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE 1CHO POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ZYMOGEN OF 1CHO THIS ENZYME BY EXCISION OF RESIDUES 14-15 AND 147-148. TO 1CHO ASSIGN SEPARATE CHAIN IDENTIFIERS TO THE THREE CHAINS 1CHO WOULD OBSCURE THIS RELATIONSHIP AND SO THIS WAS NOT DONE. 1CHO CHAIN TERMINATOR RECORDS WERE INSERTED AFTER RESIDUES 146 1CHO AND 245 TO INDICATE EXPLICIT TERMINI AND THE SPECIAL CODE 1CHO EXC WAS USED IN THE SEQRES RECORDS TO DENOTE THE EXCISIONS. 1CHO
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDChemical formula
150 %sat1reservoir(NH4)2SO4
250 mM1reservoirK2HPO4

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 24883 / Biso Wilson estimate: 17.9 Å2 / Num. measured all: 27564

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å /
RfactorNum. reflection
obs0.168 19178
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 0 221 2371
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.012
X-RAY DIFFRACTIONp_angle_d0.0410.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.036
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0170.012
X-RAY DIFFRACTIONp_chiral_restr0.1760.08
X-RAY DIFFRACTIONp_singtor_nbd0.3310.3
X-RAY DIFFRACTIONp_multtor_nbd0.1880.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2360.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.33
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(I): 1 / Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 19178 / Rfactor obs: 0.168
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://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