[English] 日本語
Yorodumi
- PDB-2ql9: Crystal Structure of Caspase-7 with inhibitor AC-DQMD-CHO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ql9
TitleCrystal Structure of Caspase-7 with inhibitor AC-DQMD-CHO
Components
  • (Caspase-7Caspase 7) x 2
  • Inhibitor AC-DQMD-CHO
  • PEPTIDE QGHGE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEASE / APOPTOSIS / THIOL PROTEASE / ZYMOGEN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / response to UV / striated muscle cell differentiation / protein catabolic process / protein processing / heart development / peptidase activity / neuron apoptotic process / cellular response to lipopolysaccharide / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-like / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues ...Caspase-like / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AC-DQMD-CHO / CITRIC ACID / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsAgniswamy, J. / Fang, B. / Weber, I.
CitationJournal: Febs J. / Year: 2007
Title: Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis.
Authors: Agniswamy, J. / Fang, B. / Weber, I.T.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-7
B: Caspase-7
C: Caspase-7
D: Caspase-7
E: Inhibitor AC-DQMD-CHO
F: Inhibitor AC-DQMD-CHO
G: PEPTIDE QGHGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5948
Polymers63,4027
Non-polymers1921
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.158, 87.158, 187.416
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Caspase-7 / Caspase 7 / CASP-7 / ICE-like apoptotic protease 3 / ICE-LAP3 / Apoptotic protease Mch-3 / CMH-1


Mass: 19564.598 Da / Num. of mol.: 2 / Fragment: P20 subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: PET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P55210, caspase-7
#2: Protein Caspase-7 / Caspase 7 / CASP-7 / ICE-like apoptotic protease 3 / ICE-LAP3 / Apoptotic protease Mch-3 / CMH-1


Mass: 11352.862 Da / Num. of mol.: 2 / Fragment: P10 subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: PET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P55210, caspase-7

-
Protein/peptide , 2 types, 3 molecules EFG

#3: Protein/peptide Inhibitor AC-DQMD-CHO


Type: Peptide-like / Class: Inhibitor / Mass: 519.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: AC-DQMD-CHO
#4: Protein/peptide PEPTIDE QGHGE


Mass: 527.508 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 2 types, 297 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTHE INHIBITOR IS COVALENTLY CONNECTED TO CYS OF THE ENZYME TO FORM A HEMITHIOKETAL

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 14.5% PEG 3350, 0.3M diammonium hydrogen citrate, 10mM DTT, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2007
RadiationMonochromator: si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 41654 / % possible obs: 90.94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 24.01
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.23 / Num. unique all: 3638 / % possible all: 80.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F1J

1f1j


Resolution: 2.14→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2086 -random
Rwork0.191 ---
obs0.197 40671 90.94 %-
all-44723 --
Refinement stepCycle: LAST / Resolution: 2.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 13 296 4134

+
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