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- PDB-8co0: Three dimensional structure of human carbonic anhydrase IX in com... -

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Basic information

Entry
Database: PDB / ID: 8co0
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
Chem-V8O / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLeitans, J. / Tars, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Atropo/Tropo Flexibility: A Tool for Design and Synthesis of Self-Adaptable Inhibitors of Carbonic Anhydrases and Their Antiproliferative Effect.
Authors: Ivanova, J.N. / Nocentini, A. / Tars, K. / Leita Ns, J.N. / Dvinskis, E. / Kazaks, A. / Domraceva, I. / Supuran, C.T. / Zalubovskis, R.
History
DepositionFeb 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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
C: Carbonic anhydrase 9
E: Carbonic anhydrase 9
G: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,90316
Polymers112,7474
Non-polymers2,15612
Water10,503583
1
A: Carbonic anhydrase 9
C: Carbonic anhydrase 9
hetero molecules

E: Carbonic anhydrase 9
G: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,90316
Polymers112,7474
Non-polymers2,15612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_544-x+y+1/3,-x-1/3,z-1/31
Buried area7610 Å2
ΔGint-52 kcal/mol
Surface area39140 Å2
Unit cell
Length a, b, c (Å)152.951, 152.951, 172.438
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 / 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: 28186.711 Da / Num. of mol.: 4 / Mutation: C41S, N213Q
Source method: isolated from a genetically manipulated source
Details: two dimers / Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Cell line (production host): Pichia pastoris / 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-V8O / 5-(5-methyl-6-quinolin-5-yl-pyridin-3-yl)thiophene-2-sulfonamide


Mass: 381.471 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H15N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 3.46 Å3/Da / Density % sol: 64.46 %
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: 2.3→29.93 Å / Num. obs: 66667 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 8.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4658 / % possible all: 94.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0350 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.93 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.752 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21231 3427 5.1 %RANDOM
Rwork0.16044 ---
obs0.16307 63380 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.648 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7910 0 0 583 8493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128170
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167228
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.66511169
X-RAY DIFFRACTIONr_angle_other_deg0.481.54616865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89151000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.4931071
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.193101185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021637
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_it3.3694.4154012
X-RAY DIFFRACTIONr_mcbond_other3.3694.4154012
X-RAY DIFFRACTIONr_mcangle_it4.8676.6125008
X-RAY DIFFRACTIONr_mcangle_other4.8676.6135009
X-RAY DIFFRACTIONr_scbond_it4.1924.7694158
X-RAY DIFFRACTIONr_scbond_other4.1914.774159
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1917.0146162
X-RAY DIFFRACTIONr_long_range_B_refined7.94855.7228487
X-RAY DIFFRACTIONr_long_range_B_other7.95255.0328374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 275 -
Rwork0.235 4622 -
obs--100 %

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