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- PDB-6fe1: Three dimensional structure of human carbonic anhydrase IX in com... -

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Basic information

Entry
Database: PDB / ID: 6fe1
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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-V14 / 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: Oncotarget / Year: 2018
Title: Novel fluorinated carbonic anhydrase IX inhibitors reduce hypoxia-induced acidification and clonogenic survival of cancer cells.
Authors: Kazokaite, J. / Niemans, R. / Dudutiene, V. / Becker, H.M. / Leitans, J. / Zubriene, A. / Baranauskiene, L. / Gondi, G. / Zeidler, R. / Matuliene, J. / Tars, K. / Yaromina, A. / Lambin, P. / ...Authors: Kazokaite, J. / Niemans, R. / Dudutiene, V. / Becker, H.M. / Leitans, J. / Zubriene, A. / Baranauskiene, L. / Gondi, G. / Zeidler, R. / Matuliene, J. / Tars, K. / Yaromina, A. / Lambin, P. / Dubois, L.J. / Matulis, D.
History
DepositionDec 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.2Oct 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)114,73012
Polymers112,6914
Non-polymers2,0408
Water13,259736
1
A: Carbonic anhydrase 9
B: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3656
Polymers56,3452
Non-polymers1,0204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area20420 Å2
MethodPISA
2
C: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3656
Polymers56,3452
Non-polymers1,0204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-10 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.020, 152.020, 172.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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-V14 / 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 444.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H23F3N2O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 3.42 Å3/Da / Density % sol: 64.05 %
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)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.95→25.18 Å / Num. obs: 107506 / % possible obs: 99.4 % / Redundancy: 3 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.501 / Num. unique obs: 15617 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IAI

3iai


Resolution: 1.95→25.18 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.042 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21643 5404 5 %RANDOM
Rwork0.18204 ---
obs0.18377 102100 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.738 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å2-0 Å2
2--0.88 Å2-0 Å2
3----2.85 Å2
Refinement stepCycle: 1 / Resolution: 1.95→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7667 0 116 736 8519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198077
X-RAY DIFFRACTIONr_bond_other_d0.0020.027329
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.98211028
X-RAY DIFFRACTIONr_angle_other_deg0.942317012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88323.077364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.809151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9051568
X-RAY DIFFRACTIONr_chiral_restr0.0820.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218925
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021651
X-RAY DIFFRACTIONr_mcbond_it2.2173.7943983
X-RAY DIFFRACTIONr_mcbond_other2.2163.7933982
X-RAY DIFFRACTIONr_mcangle_it3.4875.6584944
X-RAY DIFFRACTIONr_mcangle_other3.4875.6594945
X-RAY DIFFRACTIONr_scbond_it2.6614.0934094
X-RAY DIFFRACTIONr_scbond_other2.6614.0944095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2946.0576074
X-RAY DIFFRACTIONr_long_range_B_refined7.08245.7878902
X-RAY DIFFRACTIONr_long_range_B_other6.99345.2148704
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 338 -
Rwork0.308 7470 -
obs--98.37 %

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