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- PDB-9fjq: Structure of human carbonic anhydrase II complexed with 4-benzyl-... -

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Basic information

Entry
Database: PDB / ID: 9fjq
TitleStructure of human carbonic anhydrase II complexed with 4-benzyl-5,7,8-trifluoro-3,4-dihydro-2H-benzo[b][1,4]thiazine-6-sulfonamide 1,1-dioxide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / DRUG DESIGN / CARBONIC ANHYDRASE / BENZENESULFONAMIDE
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsManakova, E.N. / Grazulis, S. / Paketuryte, V. / Smirnov, A. / Vaskevicius, A. / Trumpickaite, G.
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
DepositionMay 31, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8394
Polymers29,2891
Non-polymers5503
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint1 kcal/mol
Surface area11460 Å2
Unit cell
Length a, b, c (Å)42.188, 41.323, 71.913
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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.: 1 / Source method: obtained synthetically / Formula: C15H13F3N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: Bicine pH 9 0.1M, Sodium Malonate pH 7 2M / PH range: 7-9

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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: 1.1→69.72 Å / Num. obs: 95773 / % possible obs: 98.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 11.507 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Χ2: 1 / Net I/av σ(I): 2.8 / Net I/σ(I): 9.5
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4478 / CC1/2: 0.7 / Rpim(I) all: 0.416 / Rrim(I) all: 1.085 / Χ2: 1.02 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSVERSION Jan 10, 2022 BUILT=20220220data reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→40.9 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16787 9609 10 %RANDOM
Rwork0.1458 ---
obs0.14804 86132 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.073 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0 Å20.23 Å2
2--0.25 Å20 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.1→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 31 291 2371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122317
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.821.6513182
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0395297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46723.982113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.682157
X-RAY DIFFRACTIONr_chiral_restr0.1210.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021841
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_it1.9121.6151123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.462.4431428
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0381.9071194
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.00523.8093631
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.00632317
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 662 -
Rwork0.235 5961 -
obs--92.01 %

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