[English] 日本語
Yorodumi
- PDB-6h38: The crystal structure of human carbonic anhydrase VII in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h38
TitleThe crystal structure of human carbonic anhydrase VII in complex with 4-[(4-fluorophenyl)methyl]-1-piperazinyl]benzenesulfonamide.
ComponentsCarbonic anhydrase 7
KeywordsLYASE / Protein-Inhibitor Binding
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding ...positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase VII / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. ...Carbonic anhydrase VII / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-FKK / Carbonic anhydrase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsBuemi, M.R. / Di Fiore, A. / De Luca, L. / Ferro, S. / Mancuso, F. / Monti, S.M. / Buonanno, M. / Angeli, A. / Russo, E. / De Sarro, G. ...Buemi, M.R. / Di Fiore, A. / De Luca, L. / Ferro, S. / Mancuso, F. / Monti, S.M. / Buonanno, M. / Angeli, A. / Russo, E. / De Sarro, G. / Supuran, C.T. / De Simone, G. / Gitto, R.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Exploring structural properties of potent human carbonic anhydrase inhibitors bearing a 4-(cycloalkylamino-1-carbonyl)benzenesulfonamide moiety.
Authors: Buemi, M.R. / Di Fiore, A. / De Luca, L. / Angeli, A. / Mancuso, F. / Ferro, S. / Monti, S.M. / Buonanno, M. / Russo, E. / De Sarro, G. / De Simone, G. / Supuran, C.T. / Gitto, R.
History
DepositionJul 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5535
Polymers30,9261
Non-polymers6274
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-5 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.100, 89.240, 44.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Carbonic anhydrase 7 / Carbonate dehydratase VII / Carbonic anhydrase VII / CA-VII


Mass: 30925.693 Da / Num. of mol.: 1 / Mutation: C183S, C217S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P43166, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FKK / 4-[4-[(4-fluorophenyl)methyl]piperazin-1-yl]carbonylbenzenesulfonamide


Mass: 377.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20FN3O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% v/v Peg3350, 0.2 M Ammonium acetate, 0.1 M Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 30, 2018 / Details: Mirror
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→34 Å / Num. obs: 28527 / % possible obs: 96.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Net I/σ(I): 27.3
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.6 / Rpim(I) all: 0.34 / Rrim(I) all: 0.663 / % possible all: 90.2

-
Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6G4T

6g4t


Resolution: 1.7→34 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.245 --
Rwork0.193 --
obs-26198 92.5 %
Refinement stepCycle: LAST / Resolution: 1.7→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 39 144 2238

+
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