[English] 日本語
Yorodumi
- PDB-7ywt: human Carbonic Anhydrase II in complex with 4-oxo-N-(4-sulfamoylp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ywt
Titlehuman Carbonic Anhydrase II in complex with 4-oxo-N-(4-sulfamoylphenyl)-1,3,4,6,7,11b-hexahydro-2H-pyrazino[2,1-a]isoquinoline-2-carboxamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase II / sulfonamide / metalloenzyme / praziquantel
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-I6U / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.106 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Enzyme Inhib Med Chem / Year: 2022
Title: Development of Praziquantel sulphonamide derivatives as antischistosomal drugs.
Authors: Angeli, A. / Ferraroni, M. / Carta, F. / Haberli, C. / Keiser, J. / Costantino, G. / Supuran, C.T.
History
DepositionFeb 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8474
Polymers29,2891
Non-polymers5583
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-7 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.420, 41.480, 72.040
Angle α, β, γ (deg.)90.000, 104.445, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-I6U / (11~{b}~{R})-4-oxidanylidene-~{N}-(4-sulfamoylphenyl)-3,6,7,11~{b}-tetrahydro-1~{H}-pyrazino[2,1-a]isoquinoline-2-carboxamide


Mass: 400.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5 M sodium citrate, 0.1 M Tris pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.106→48 Å / Num. obs: 95824 / % possible obs: 98.8 % / Redundancy: 6.14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.068 / Net I/σ(I): 16.4
Reflection shellResolution: 1.11→1.13 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 6872 / CC1/2: 0.727 / Rrim(I) all: 1.062 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIK

4fik


Resolution: 1.106→48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.454 / SU ML: 0.022 / Cross valid method: NONE / ESU R: 0.031 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1774 4688 4.893 %
Rwork0.1615 91129 -
all0.162 --
obs-95817 98.829 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.144 Å20 Å2-0.103 Å2
2---0.019 Å20 Å2
3---0.191 Å2
Refinement stepCycle: LAST / Resolution: 1.106→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 35 248 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132203
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162038
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.6363005
X-RAY DIFFRACTIONr_angle_other_deg1.5071.6034736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1225274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15123.853109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98915366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.975157
X-RAY DIFFRACTIONr_chiral_restr0.1030.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.2470.2422
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21973
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21041
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21034
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2148
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3210.214
X-RAY DIFFRACTIONr_nbd_other0.2450.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.221
X-RAY DIFFRACTIONr_mcbond_it1.3641.0591050
X-RAY DIFFRACTIONr_mcbond_other1.3531.0531047
X-RAY DIFFRACTIONr_mcangle_it2.0831.5911312
X-RAY DIFFRACTIONr_mcangle_other2.0831.5931313
X-RAY DIFFRACTIONr_scbond_it2.2971.2991153
X-RAY DIFFRACTIONr_scbond_other2.2961.31154
X-RAY DIFFRACTIONr_scangle_it3.4581.8561684
X-RAY DIFFRACTIONr_scangle_other3.4571.8581685
X-RAY DIFFRACTIONr_lrange_it4.20213.3752475
X-RAY DIFFRACTIONr_lrange_other4.20213.3832475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.106-1.1350.293070.2826556X-RAY DIFFRACTION96.2958
1.135-1.1660.2313270.2316424X-RAY DIFFRACTION97.0669
1.166-1.20.2093080.2066247X-RAY DIFFRACTION97.3129
1.2-1.2360.213060.1936137X-RAY DIFFRACTION97.7397
1.236-1.2770.1853180.1845944X-RAY DIFFRACTION98.3046
1.277-1.3220.1953350.1655789X-RAY DIFFRACTION98.9018
1.322-1.3720.1772940.1595604X-RAY DIFFRACTION99.3096
1.372-1.4280.1812840.1565414X-RAY DIFFRACTION99.6154
1.428-1.4910.1592940.1525181X-RAY DIFFRACTION99.6905
1.491-1.5640.1582650.1434997X-RAY DIFFRACTION99.7346
1.564-1.6480.1552460.1414739X-RAY DIFFRACTION99.9599
1.648-1.7480.1672080.1474540X-RAY DIFFRACTION99.9789
1.748-1.8690.1522170.1474228X-RAY DIFFRACTION99.955
1.869-2.0190.1841970.1493966X-RAY DIFFRACTION99.7604
2.019-2.2110.1711920.1483610X-RAY DIFFRACTION99.7638
2.211-2.4720.1621760.1473313X-RAY DIFFRACTION99.7427
2.472-2.8530.1551560.1552915X-RAY DIFFRACTION99.8375
2.853-3.4930.181110.162493X-RAY DIFFRACTION99.6937
3.493-4.9340.167980.1491932X-RAY DIFFRACTION99.8524
4.934-480.245490.1951100X-RAY DIFFRACTION98.4576

+
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