[English] 日本語
Yorodumi
- PDB-9r8y: Three dimensional structure of human carbonic anhydrase IX in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r8y
TitleThree dimensional structure of human carbonic anhydrase IX in complex with sulfonamide
ComponentsCarbonic anhydrase 9
KeywordsLYASE / CA IX / CA 9 / CARBONIC ANHYDRASE IX / CARBONIC ANHYDRASE 9
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane ...Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / nucleolus / 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 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLeitans, J. / Tars, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)5.2.1.1.i.0/2/24/I/CFLA/001European Union
CitationJournal: J.Med.Chem. / Year: 2025
Title: Affinity and Selectivity of Protein-Ligand Recognition: A Minor Chemical Modification Changes Carbonic Anhydrase Binding Profile.
Authors: Zaksauskas, A. / Paketuryte-Latve, V. / Jankunaite, A. / Capkauskaite, E. / Becart, Y. / Smirnov, A. / Pospisilova, K. / Leitans, J. / Brynda, J. / Kazaks, A. / Baranauskiene, L. / Manakova, ...Authors: Zaksauskas, A. / Paketuryte-Latve, V. / Jankunaite, A. / Capkauskaite, E. / Becart, Y. / Smirnov, A. / Pospisilova, K. / Leitans, J. / Brynda, J. / Kazaks, A. / Baranauskiene, L. / Manakova, E. / Grazulis, S. / Kairys, V. / Tars, K. / Rezacova, P. / Matulis, D.
History
DepositionMay 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 9
B: Carbonic anhydrase 9
C: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,10212
Polymers112,3584
Non-polymers1,7448
Water12,448691
1
A: Carbonic anhydrase 9
B: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0516
Polymers56,1792
Non-polymers8724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area20410 Å2
MethodPISA
2
C: Carbonic anhydrase 9
hetero molecules

D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0516
Polymers56,1792
Non-polymers8724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x+y+1/3,-x+2/3,z-1/31
Buried area1610 Å2
ΔGint-10 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.921, 151.921, 173.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

-
Components

#1: Protein
Carbonic anhydrase 9 / Carbonate dehydratase IX / Carbonic anhydrase IX / CA-IX / CAIX / Membrane antigen MN / P54/58N / ...Carbonate dehydratase IX / Carbonic anhydrase IX / CA-IX / CAIX / Membrane antigen MN / P54/58N / Renal cell carcinoma-associated antigen G250 / RCC-associated antigen G250 / pMW1


Mass: 28089.598 Da / Num. of mol.: 4 / Mutation: C41S, N213Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Production host: Komagataella pastoris (fungus) / References: UniProt: Q16790, 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-A1JDL / ~{N}-butyl-4-cyclohexylsulfanyl-3-sulfamoyl-benzamide


Mass: 370.530 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H26N2O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE)

-
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: Oct 2, 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: 1.95→47.81 Å / Num. obs: 108927 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 22.404 Å2 / Rmerge(I) obs: 0.218 / Net I/σ(I): 7.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.298 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5418 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.84 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25357 5484 5.2 %RANDOM
Rwork0.21284 ---
obs0.21496 99209 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.692 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å2-0 Å2
2--0.46 Å20 Å2
3----1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.95→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7381 0 100 691 8172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127681
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167185
X-RAY DIFFRACTIONr_angle_refined_deg1.721.85710485
X-RAY DIFFRACTIONr_angle_other_deg0.5681.73816553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9735956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.476563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.436101142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021767
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_it3.0893.1713836
X-RAY DIFFRACTIONr_mcbond_other3.0883.1713836
X-RAY DIFFRACTIONr_mcangle_it4.5145.6894788
X-RAY DIFFRACTIONr_mcangle_other4.5145.6894789
X-RAY DIFFRACTIONr_scbond_it3.6193.5063845
X-RAY DIFFRACTIONr_scbond_other3.6193.5063846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5426.2935698
X-RAY DIFFRACTIONr_long_range_B_refined7.63831.68055
X-RAY DIFFRACTIONr_long_range_B_other7.58530.67903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 411 -
Rwork0.323 7561 -
obs--99.18 %

+
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