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- PDB-7q0d: Human carbonic anhydrase I in complex with Methyl 2-(benzenesulfo... -

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Basic information

Entry
Database: PDB / ID: 7q0d
TitleHuman carbonic anhydrase I in complex with Methyl 2-(benzenesulfonyl)-4-chloro-5-sulfamoylbenzoate
ComponentsCarbonic anhydrase 1
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol
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-84Z / ACETATE ION / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 1
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,84834
Polymers57,8122
Non-polymers3,03632
Water15,061836
1
A: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,29416
Polymers28,9061
Non-polymers1,38815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,55418
Polymers28,9061
Non-polymers1,64817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.039, 73.235, 120.473
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28906.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: P00915, carbonic anhydrase

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Non-polymers , 6 types, 868 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-84Z / methyl 4-chloranyl-2-(phenylsulfonyl)-5-sulfamoyl-benzoate


Mass: 389.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12ClNO6S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 836 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer: 0.1 M Tris-HCl (pH 8.5), 0.2 M ammonium acetate and 24% PEG4000

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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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.243→62.039 Å / Num. all: 151876 / Num. obs: 151876 / % possible obs: 98.3 % / Redundancy: 12.9 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.083 / Rsym value: 0.075 / Net I/av σ(I): 3.2 / Net I/σ(I): 22 / Num. measured all: 1961733
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.243-1.31110.1943.8199410.0630.2160.19489.6
1.31-1.3913.10.1644.4211400.0490.1810.16499.9
1.39-1.4912.90.1315.3199000.040.1460.13199.9
1.49-1.613.30.1036.3185480.0310.1160.10399.8
1.6-1.7613.10.0876.9170720.0270.0990.08799.8
1.76-1.9713.60.0757.5155220.0230.0850.07599.8
1.97-2.2713.30.0697.7137140.0210.0770.06999.6
2.27-2.7813.60.0678116630.020.0740.06799.8
2.78-3.9313.30.0686.791400.020.0750.06899.7
3.93-62.03912.80.0755.952360.0230.0820.07599.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CAB

1cab
PDB Unreleased entry


Resolution: 1.24→55.16 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1577 15031 9.9 %RANDOM
Rwork0.1309 ---
obs0.1335 136749 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 691.13 Å2 / Biso mean: 17.893 Å2 / Biso min: 5.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.24→55.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 234 869 5121
Biso mean--30.05 32.01 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0194766
X-RAY DIFFRACTIONr_angle_refined_deg2.421.9686505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9685599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22924.907214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77515708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg211516
X-RAY DIFFRACTIONr_chiral_restr0.1710.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0213777
X-RAY DIFFRACTIONr_rigid_bond_restr9.39334766
X-RAY DIFFRACTIONr_sphericity_free28.3365505
X-RAY DIFFRACTIONr_sphericity_bonded20.35754992
LS refinement shellResolution: 1.243→1.275 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.163 921 -
Rwork0.128 8061 -
all-8982 -
obs--79.82 %

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