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- PDB-9f2o: Structure of human carbonic anhydrase XII complexed with 3-(cyclo... -

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Basic information

Entry
Database: PDB / ID: 9f2o
TitleStructure of human carbonic anhydrase XII complexed with 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5- methoxybenzenesulfonamide
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
: / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsManakova, E.N. / Grazulis, S. / Paketuryte, V. / Smirnov, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-Discovery871037European Union
CitationJournal: To Be Published
Title: Structure of human carbonic anhydrase XII complexed with 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5- methoxybenzenesulfonamide
Authors: Manakova, E.N. / Grazulis, S. / Paketuryte, V. / Smirnov, A.
History
DepositionApr 23, 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

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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)123,13132
Polymers119,6694
Non-polymers3,46128
Water23,2751292
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,52515
Polymers59,8352
Non-polymers1,69113
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)61,60517
Polymers59,8352
Non-polymers1,77115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.391, 73.947, 91.361
Angle α, β, γ (deg.)90.00, 108.88, 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: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43570, carbonic anhydrase

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Non-polymers , 6 types, 1320 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.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-A1H89 / 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5- methoxybenzenesulfonamide / 3-(cyclooctylamino)-2,6-bis(fluoranyl)-5-methoxy-4-(3-oxidanylpropylsulfonyl)benzenesulfonamide


Mass: 470.552 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H28F2N2O6S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1292 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammonium Citrate pH 7.0 0.1M; Ammonium Sulfate 0.2M; PEG4000 26%
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: 1.12→86.44 Å / Num. obs: 357013 / % possible obs: 96.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 9.91 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Χ2: 0.98 / Net I/av σ(I): 2.5 / Net I/σ(I): 10.9
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9280 / CC1/2: 0.767 / Rpim(I) all: 0.336 / Rrim(I) all: 0.526 / Χ2: 0.98 / % possible all: 50.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→56.26 Å / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034
RfactorNum. reflection% reflectionSelection details
Rfree0.16363 35770 10 %RANDOM
Rwork0.13644 ---
obs0.13915 321195 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 16.951 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0.01 Å2
2--0.63 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.12→56.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8363 0 207 1292 9862
LS refinement shellResolution: 1.122→1.151 Å
RfactorNum. reflection% reflection
Rfree0.27 1649 -
Rwork0.251 15396 -
obs--62.23 %

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