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- PDB-6qn2: Three dimensional structure of human carbonic anhydrase IX in com... -

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Basic information

Entry
Database: PDB / ID: 6qn2
TitleThree dimensional structure of human carbonic anhydrase IX in complex with benzenesulfonamide
ComponentsCarbonic anhydrase 9
KeywordsLYASE
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
Chem-J92 / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLeitans, J. / Tars, K.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms.
Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Paketuryte, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Manakova, E. / Grazulis, S. / Tars, K. / Matulis, D.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 6, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_contact_author / pdbx_database_proc / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)114,74812
Polymers112,6914
Non-polymers2,0588
Water11,494638
1
A: Carbonic anhydrase 9
C: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3746
Polymers56,3452
Non-polymers1,0294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-9 kcal/mol
Surface area20640 Å2
MethodPISA
2
B: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3746
Polymers56,3452
Non-polymers1,0294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-10 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.640, 152.640, 172.840
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
11C-430-

HOH

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Components

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


Mass: 28172.684 Da / Num. of mol.: 4 / Mutation: C42S
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-J92 / methyl 4-[(4-chloranyl-2-cyclohexylsulfanyl-5-sulfamoyl-phenyl)carbonylamino]butanoate


Mass: 448.985 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H25ClN2O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: CRYSTALLIZATION CONDITIONS: 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)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97776 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.95→76.32 Å / Num. obs: 109432 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.116 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 15964 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FE2

6fe2


Resolution: 1.95→76.32 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.107 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25328 5517 5 %RANDOM
Rwork0.21278 ---
obs0.21481 103914 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.237 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→76.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7729 0 116 638 8483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138060
X-RAY DIFFRACTIONr_bond_other_d0.0030.0177336
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.66810985
X-RAY DIFFRACTIONr_angle_other_deg1.3781.58117013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76321.153425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.464151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6461565
X-RAY DIFFRACTIONr_chiral_restr0.0720.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021712
X-RAY DIFFRACTIONr_mcbond_it3.2953.9043990
X-RAY DIFFRACTIONr_mcbond_other3.2953.9043989
X-RAY DIFFRACTIONr_mcangle_it4.8015.8354944
X-RAY DIFFRACTIONr_mcangle_other4.85.8354945
X-RAY DIFFRACTIONr_scbond_it3.9014.2954070
X-RAY DIFFRACTIONr_scbond_other3.94.2954071
X-RAY DIFFRACTIONr_scangle_other5.8796.2996042
X-RAY DIFFRACTIONr_long_range_B_refined7.98247.1488837
X-RAY DIFFRACTIONr_long_range_B_other7.95946.938718
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 430 -
Rwork0.489 7632 -
obs--99.99 %

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