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- PDB-6tl6: Three dimensional structure of human carbonic anhydrase IX in com... -

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Basic information

Entry
Database: PDB / ID: 6tl6
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 / 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
naphthalene-2-sulfonamide / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)114,02214
Polymers112,7474
Non-polymers1,27510
Water11,890660
1
A: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0117
Polymers56,3732
Non-polymers6375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 9
C: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0117
Polymers56,3732
Non-polymers6375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.902, 152.902, 171.584
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-436-

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
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: isolated from a natural source / Formula: Zn
#3: Chemical
ChemComp-MUE / naphthalene-2-sulfonamide


Mass: 207.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.45 Å3/Da / Density % sol: 64.33 %
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% ...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), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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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: 2.144→104.806 Å / Num. obs: 82019 / % possible obs: 100 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.5
Reflection shellResolution: 2.144→2.181 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.116 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4095 / % possible all: 99.9

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Processing

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

6fe2


Resolution: 2.15→48.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19505 4338 5.3 %RANDOM
Rwork0.16058 ---
obs0.16249 77488 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.15→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7729 0 72 660 8461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138015
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177292
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.65910925
X-RAY DIFFRACTIONr_angle_other_deg2.4781.56716899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2175980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08121.185422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.672151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3451564
X-RAY DIFFRACTIONr_chiral_restr0.0780.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028984
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021720
X-RAY DIFFRACTIONr_mcbond_it3.8954.4743992
X-RAY DIFFRACTIONr_mcbond_other3.8954.4733991
X-RAY DIFFRACTIONr_mcangle_it5.6116.6684948
X-RAY DIFFRACTIONr_mcangle_other5.616.6694949
X-RAY DIFFRACTIONr_scbond_it4.8064.9384023
X-RAY DIFFRACTIONr_scbond_other4.8064.9384024
X-RAY DIFFRACTIONr_scangle_other7.0867.2585978
X-RAY DIFFRACTIONr_long_range_B_refined9.61153.2798627
X-RAY DIFFRACTIONr_long_range_B_other9.61652.9268492
LS refinement shellResolution: 2.15→2.202 Å
RfactorNum. reflection% reflection
Rfree0.249 256 -
Rwork0.221 5736 -
obs--100 %

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