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- PDB-6tl5: Three dimensional structure of human carbonic anhydrase IX in com... -

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Basic information

Entry
Database: PDB / ID: 6tl5
TitleThree dimensional structure of human carbonic anhydrase IX in complex with sulfonamide
ComponentsCarbonic anhydrase 9
KeywordsLYASE
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process ...Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / 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
3,5-diphenylbenzenesulfonamide / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsLeitans, J. / Tars, K.
CitationJournal: Biophys.J. / Year: 2020
Title: Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle.
Authors: Dudutiene, V. / Zubriene, A. / Kairys, V. / Smirnov, A. / Smirnoviene, J. / Leitans, J. / Kazaks, A. / Tars, K. / Manakova, L. / Grazulis, S. / Matulis, D.
History
DepositionDec 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
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
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)114,24612
Polymers112,7474
Non-polymers1,4998
Water9,242513
1
A: Carbonic anhydrase 9
B: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1236
Polymers56,3732
Non-polymers7504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-10 kcal/mol
Surface area20540 Å2
MethodPISA
2
C: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1236
Polymers56,3732
Non-polymers7504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-11 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.060, 152.060, 172.090
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
11B-442-

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: 28186.711 Da / Num. of mol.: 4 / Mutation: C42S
Source method: isolated from a genetically manipulated source
Details: All 4 chains are identical / Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Production host: Komagataella pastoris (fungus) / References: UniProt: Q16790, carbonic anhydrase
#2: Chemical
ChemComp-MKQ / 3,5-diphenylbenzenesulfonamide


Mass: 309.382 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C18H15NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.42 Å3/Da / Density % sol: 64.04 %
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), VAPOR ...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), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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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: Mar 19, 2019
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.21→76.04 Å / Num. obs: 73962 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 30.632 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.9
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / Num. unique obs: 10814 / % possible all: 99.5

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Processing

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

6fe2


Resolution: 2.21→76.04 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22151 3756 5.1 %RANDOM
Rwork0.178 ---
obs0.18027 70181 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.588 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å2-0 Å2
2--0.38 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.21→76.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7638 0 92 513 8243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137946
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177215
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.66410839
X-RAY DIFFRACTIONr_angle_other_deg2.4571.57116705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9375973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74721.214412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.945151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4181562
X-RAY DIFFRACTIONr_chiral_restr0.0720.2978
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028936
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021718
X-RAY DIFFRACTIONr_mcbond_it3.4834.4393961
X-RAY DIFFRACTIONr_mcbond_other3.4834.4383960
X-RAY DIFFRACTIONr_mcangle_it5.3276.6184911
X-RAY DIFFRACTIONr_mcangle_other5.3266.6194912
X-RAY DIFFRACTIONr_scbond_it4.0794.8363985
X-RAY DIFFRACTIONr_scbond_other4.0784.8363986
X-RAY DIFFRACTIONr_scangle_other6.3797.1385929
X-RAY DIFFRACTIONr_long_range_B_refined9.38452.9498472
X-RAY DIFFRACTIONr_long_range_B_other9.3852.8248393
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 284 -
Rwork0.402 5131 -
obs--98.87 %

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