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- PDB-7q0c: Mimic carbonic anhydrase IX in complex with Methyl 2-chloro-4-(cy... -

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Basic information

Entry
Database: PDB / ID: 7q0c
TitleMimic carbonic anhydrase IX in complex with Methyl 2-chloro-4-(cyclohexylsulfanyl)-5-sulfamoylbenzoate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / 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 / one-carbon metabolic process / 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
Chem-7VZ / ACETATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsPaketuryte-Latve, V. / Smirnov, A. / Manakova, E. / Grazulis, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2021
Title: Methyl 2-Halo-4-Substituted-5-Sulfamoyl-Benzoates as High Affinity and Selective Inhibitors of Carbonic Anhydrase IX.
Authors: Zaksauskas, A. / Capkauskaite, E. / Paketuryte-Latve, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Stancaitis, L. / Mickeviciute, A. / Jachno, J. / Jezepcikas, L. / ...Authors: Zaksauskas, A. / Capkauskaite, E. / Paketuryte-Latve, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Stancaitis, L. / Mickeviciute, A. / Jachno, J. / Jezepcikas, L. / Linkuviene, V. / Sakalauskas, A. / Manakova, E. / Grazulis, S. / Matuliene, J. / Tars, K. / Matulis, D.
History
DepositionOct 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5609
Polymers58,4862
Non-polymers1,0747
Water10,845602
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8095
Polymers29,2431
Non-polymers5664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7504
Polymers29,2431
Non-polymers5073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.060, 41.348, 72.029
Angle α, β, γ (deg.)90.000, 104.140, 90.000
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29242.992 Da / Num. of mol.: 2 / Mutation: A65S, N67Q, I91L, F130V, V134L, L203A.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): L21(DE3) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 609 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-7VZ / methyl 2-chloranyl-4-cyclohexylsulfanyl-5-sulfamoyl-benzoate


Mass: 363.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18ClNO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer: 0.1M sodium bicine (pH 9.0), 0.2 M ammonium sulfate and 2M sodium malonate (pH 7.0)

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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: P14 (MX2) / Wavelength: 0.9755 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.12→41.35 Å / Num. obs: 146352 / % possible obs: 81.3 % / Redundancy: 3.8 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.063 / Rsym value: 0.042 / Net I/av σ(I): 3.4 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.122-1.183.60.1026.7135030.0790.1530.10251.4
1.18-1.253.70.097.8197550.0690.1340.0979.3
1.25-1.343.90.07110201270.0550.110.07186.1
1.34-1.453.90.05313.3186760.0430.0850.05386.1
1.45-1.593.90.0416.8173420.0340.0670.0486.5
1.59-1.773.90.03320.2157650.0280.0550.03387.4
1.77-2.053.90.02921.1144040.0230.0460.02990.1
2.05-2.513.90.02723.2121650.0210.0420.02790.4
2.51-3.553.90.03111.795040.0230.0450.03191.3
3.55-41.3483.80.0616.251110.0440.0870.06189.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLJ

3hlj


Resolution: 1.12→41.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 14494 9.9 %RANDOM
Rwork0.1603 ---
obs0.1637 131858 81.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 357.51 Å2 / Biso mean: 18.286 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å21.03 Å2-0.41 Å2
2---0.41 Å20.96 Å2
3----0.75 Å2
Refinement stepCycle: final / Resolution: 1.12→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 58 602 4739
Biso mean--15.64 30.88 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194627
X-RAY DIFFRACTIONr_angle_refined_deg2.5321.9636333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1725586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02724.977213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89515770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.671516
X-RAY DIFFRACTIONr_chiral_restr0.520.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213656
X-RAY DIFFRACTIONr_rigid_bond_restr20.99734627
X-RAY DIFFRACTIONr_sphericity_free28.4055355
X-RAY DIFFRACTIONr_sphericity_bonded25.22354724
LS refinement shellResolution: 1.122→1.152 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 483 -
Rwork0.2 4767 -
all-5250 -
obs--39.49 %

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