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- PDB-6yqt: CRYSTAL STRUCTURE OF HUMAN CA II IN COMPLEX WITH A SULFONAMIDE DE... -

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Basic information

Entry
Database: PDB / ID: 6yqt
TitleCRYSTAL STRUCTURE OF HUMAN CA II IN COMPLEX WITH A SULFONAMIDE DERIVATIVE OF 2-MERCAPTOBENZOXAZOLE
ComponentsCarbonic anhydrase 2
KeywordsLYASE / 2-mercaptobenzoxazole-5-sulfonamide / carbonic anhydrase / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / 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-P9E / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsAlterio, V. / De Simone, G. / Esposito, D.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationMOLIM ONCOBRAIN LAB Italy
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: 2-Mercaptobenzoxazoles: a class of carbonic anhydrase inhibitors with a novel binding mode to the enzyme active site.
Authors: Bozdag, M. / Supuran, C.T. / Esposito, D. / Angeli, A. / Carta, F. / Monti, S.M. / De Simone, G. / Alterio, V.
History
DepositionApr 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,8935
Polymers29,2891
Non-polymers6044
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint2 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.425, 41.484, 72.093
Angle α, β, γ (deg.)90.000, 104.280, 90.000
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: pETM13 / 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-P9E / 2-sulfanylidene-3~{H}-1,3-benzoxazole-5-sulfonamide


Mass: 230.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.3 M sodium citrate, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.5→35.67 Å / Num. obs: 38111 / % possible obs: 97.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Χ2: 1.047 / Net I/av σ(I): 19.9 / Net I/σ(I): 21.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.532.30.43115520.7650.3040.5320.99179
1.53-1.553.20.38417640.8450.2340.4531.03391.8
1.55-1.583.40.35817820.8630.2110.4181.08991.8
1.58-1.623.50.31218390.8910.1830.3641.05794.4
1.62-1.653.60.28818600.9090.1650.3341.07695.1
1.65-1.693.80.26218730.930.1480.3021.08896.4
1.69-1.733.90.22519080.9530.1250.2581.0997.2
1.73-1.7840.19719130.9660.1080.2261.09399.1
1.78-1.834.20.16619400.9770.0890.1891.07499.4
1.83-1.894.30.14519510.9820.0770.1651.06799.9
1.89-1.964.50.1219370.9840.0620.1361.07999.9
1.96-2.044.70.10319610.990.0520.1161.037100
2.04-2.134.90.08919640.9910.0440.11.026100
2.13-2.245.10.07719560.9950.0370.0851.078100
2.24-2.385.40.0719610.9960.0330.0771.108100
2.38-2.565.70.06719640.9960.0310.0741.01100
2.56-2.8260.05819900.9970.0250.0630.997100
2.82-3.236.40.05419530.9970.0220.0581.042100
3.23-4.076.70.04219900.9980.0170.0461.013100
4.07-35.678.60.03720530.9980.0140.0391.00199.9

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Processing

Software
NameVersionClassification
CNSv1.3refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000v714data reduction
CNS1.3phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6EQU

6equ


Resolution: 1.5→35.67 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 1024 2.6 %RANDOM SELECTION
Rwork0.1781 35472 --
obs-36496 93.1 %-
Solvent computationBsol: 41.4328 Å2
Displacement parametersBiso max: 39.12 Å2 / Biso mean: 12.7325 Å2 / Biso min: 3.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.672 Å2-0 Å20.012 Å2
2--0.449 Å20 Å2
3----1.121 Å2
Refinement stepCycle: final / Resolution: 1.5→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 33 196 2287
Biso mean--13.12 20.82 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.552
X-RAY DIFFRACTIONc_mcbond_it1.1251.5
X-RAY DIFFRACTIONc_scbond_it1.8912
X-RAY DIFFRACTIONc_mcangle_it1.6942
X-RAY DIFFRACTIONc_scangle_it2.7762.5

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