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- PDB-9fn8: Crystal structure of human carboanhydrase XII with 4-benzyl-5,7,8... -

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Basic information

Entry
Database: PDB / ID: 9fn8
TitleCrystal structure of human carboanhydrase XII with 4-benzyl-5,7,8-trifluoro-3,4-dihydro-2H-benzo[b][1,4]thiazine-6-sulfonamide 1,1-dioxide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / DRUG DESIGN / CARBONIC ANHYDRASE / BENZENESULFONAMIDE
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / apical plasma membrane / 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
: / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsManakova, E. / Paketuryte, V. / Trumpickaite, G. / Smirnov, A. / Vaskevicius, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-Discovery871037European Union
CitationJournal: Chemistry / Year: 2025
Title: Design of Rigid Compounds to Enhance Selectivity for Carbonic Anhydrase IX.
Authors: Vaskevicius, A. / Trumpickaite, G. / Parafjanovic, E. / Manakova, E. / Mickeviciute, A. / Gedgaudas, M. / Kojis, T. / Paketuryte-Latve, V. / Smirnov, A. / Baranauskiene, L. / Grazulis, S. / ...Authors: Vaskevicius, A. / Trumpickaite, G. / Parafjanovic, E. / Manakova, E. / Mickeviciute, A. / Gedgaudas, M. / Kojis, T. / Paketuryte-Latve, V. / Smirnov, A. / Baranauskiene, L. / Grazulis, S. / Zubriene, A. / Dudutiene, V. / Matulis, D.
History
DepositionJun 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,44226
Polymers119,6694
Non-polymers2,77222
Water22,1221228
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,27514
Polymers59,8352
Non-polymers1,44012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,16712
Polymers59,8352
Non-polymers1,33210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.522, 74.084, 91.838
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbonic anhydrase 12 / Carbonate dehydratase XII / Carbonic anhydrase XII / CA-XII / Tumor antigen HOM-RCC-3.1.3


Mass: 29917.318 Da / Num. of mol.: 4 / Fragment: Human Carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43570, carbonic anhydrase

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Non-polymers , 5 types, 1250 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-A1IDL / 5,7,8-tris(fluoranyl)-1,1-bis(oxidanylidene)-4-(phenylmethyl)-2,3-dihydro-1$l^{6},4-benzothiazine-6-sulfonamide


Mass: 406.400 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H13F3N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1228 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammonium Citrate pH7 0.1M; Ammonium Sulfate 0.2M; PEG4000 26% (w/v)
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.905 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 1.21→74.08 Å / Num. obs: 289181 / % possible obs: 96.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.897 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.068 / Χ2: 0.99 / Net I/av σ(I): 5.1 / Net I/σ(I): 12.7
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7736 / CC1/2: 0.728 / Rpim(I) all: 0.419 / Rrim(I) all: 0.593 / Χ2: 1.01 / % possible all: 52.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSVERSION Jan 10, 2022 BUILT=20220220data reduction
Aimlessversion 0.7.4 : 13/12/18data scaling
MOLREPVers 11.7.02; 29.05.2019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→73.37 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1695 28812 10 %RANDOM
Rwork0.13626 ---
obs0.13959 260288 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.605 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20.1 Å2
2--0.16 Å20 Å2
3----0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.21→73.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8344 0 164 1228 9736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0129383
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.65412883
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1851175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39223.613501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.471151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7881536
X-RAY DIFFRACTIONr_chiral_restr0.1240.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.027587
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.0081.464489
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5612.25713
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5331.8024894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.99322.29714873
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.19639383
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.21→1.241 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 1376 -
Rwork0.281 12543 -
obs--63.15 %

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