[English] 日本語
Yorodumi
- PDB-9r0l: Three dimensional structure of human carbonic anhydrase XII in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r0l
TitleThree dimensional structure of human carbonic anhydrase XII in complex with sulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / CA XII / CA 12 / CARBONIC ANHYDRASE XII / CARBONIC ANHYDRASE 12
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
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
: / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsEimonta, V. / Leitans, J. / Tars, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Di- meta -Substituted Fluorinated Benzenesulfonamides as Potent and Selective Anticancer Inhibitors of Carbonic Anhydrase IX and XII.
Authors: Vaskevicius, A. / Zvirblis, M. / Kurtenoka, M. / Leitans, J. / Manakova, E. / Paketuryte-Latve, V. / Kvietkauskaite, A. / Kazaks, A. / Eimonta, V. / Cerepenkaite, K. / Kazokaite-Adomaitiene, ...Authors: Vaskevicius, A. / Zvirblis, M. / Kurtenoka, M. / Leitans, J. / Manakova, E. / Paketuryte-Latve, V. / Kvietkauskaite, A. / Kazaks, A. / Eimonta, V. / Cerepenkaite, K. / Kazokaite-Adomaitiene, J. / Mickeviciu̅te, A. / Juozapaitiene, V. / Tars, K. / Grazulis, S. / Matuliene, J. / Dudutiene, V. / Shubin, K. / Matulis, D. / Zubriene, A.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,78512
Polymers119,4294
Non-polymers2,3568
Water13,836768
1
A: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8936
Polymers59,7142
Non-polymers1,1784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 12
C: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8936
Polymers59,7142
Non-polymers1,1784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.567, 76.701, 78.868
Angle α, β, γ (deg.)62.61, 79.07, 72.89
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Carbonic anhydrase 12 / Carbonate dehydratase XII / Carbonic anhydrase XII / CA-XII / Tumor antigen HOM-RCC-3.1.3


Mass: 29857.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Dimer / Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Production host: Escherichia coli (E. coli) / References: UniProt: O43570, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-A1H9A / 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5-(piperidin-1-yl)benzenesulfonamide / 3-(cyclooctylamino)-2,6-bis(fluoranyl)-4-(3-oxidanylpropylsulfonyl)-5-piperidin-1-yl-benzenesulfonamide


Mass: 523.657 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H35F2N3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.15 M MgCl2, 0.1 M NaAce (pH 5.5), 15% PEG 4000,PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS DISSOLVED IN 100% DMSO)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2024
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.45→44.41 Å / Num. obs: 158363 / % possible obs: 96.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 8.297 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 7664 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→44.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.166 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20861 8053 5.1 %RANDOM
Rwork0.18425 ---
obs0.18549 150307 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.17 Å20.1 Å2
2---0.14 Å2-0.02 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.45→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8332 0 140 768 9240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0138740
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177784
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.66511925
X-RAY DIFFRACTIONr_angle_other_deg1.5051.59818010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49651040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62923.521463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.947151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4491532
X-RAY DIFFRACTIONr_chiral_restr0.10.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029976
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022047
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3091.1494160
X-RAY DIFFRACTIONr_mcbond_other1.3081.1494159
X-RAY DIFFRACTIONr_mcangle_it2.0021.7245194
X-RAY DIFFRACTIONr_mcangle_other2.0021.7255195
X-RAY DIFFRACTIONr_scbond_it2.0541.3884580
X-RAY DIFFRACTIONr_scbond_other2.0541.3894581
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0062.0016730
X-RAY DIFFRACTIONr_long_range_B_refined4.26914.5199718
X-RAY DIFFRACTIONr_long_range_B_other4.20814.299588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 584 -
Rwork0.194 10908 -
obs--94.83 %

+
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