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- PDB-4wl4: Crystal structure of human carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4wl4
TitleCrystal structure of human carbonic anhydrase II in complex with the 6-hydroxy-chromene-2-thione inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE
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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
6-hydroxy-2H-chromene-2-thione / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsFerraroni, M.
CitationJournal: to be published
Title: New classes of carbonic anhydrase inhibitors
Authors: Ferraroni, M. / Supuran, C.T. / Carta, F. / Bozdag, M. / Scozzafava, A.
History
DepositionOct 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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)29,5954
Polymers29,2891
Non-polymers3063
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-36 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.264, 41.367, 72.276
Angle α, β, γ (deg.)90.000, 104.210, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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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 natural source / Source: (natural) Homo sapiens (human) / Organ: erythrocytes / 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-FC5 / 6-hydroxy-2H-chromene-2-thione


Mass: 178.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O2S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.6 M sodium citrate, Tris 50 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→29.1 Å / Num. obs: 78925 / % possible obs: 80.7 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / Biso Wilson estimate: 15.075 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.057 / Χ2: 1.005 / Net I/σ(I): 12.9 / Num. measured all: 272560
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.1-1.170.6870.4211.7391071573042810.55427.2
1.17-1.250.8210.3222.66224121479587260.40659
1.25-1.350.9410.2084.754471313749129120.24693.9
1.35-1.480.9760.1357.324567512695125800.15899.1
1.48-1.650.990.08711.594258311478114040.10299.4
1.65-1.910.9950.0617.53784810155100720.0799.2
1.91-2.330.9960.04624.531659861085260.05399
2.33-3.290.9970.04129.0224545671966460.04798.9
3.290.9970.03832.8914018382837780.04498.7

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
MOLREPphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P58

3p58


Resolution: 1.1→29.1 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.893 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1299 3814 4.8 %RANDOM
Rwork0.109 75094 --
obs0.11 75094 80.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.9 Å2 / Biso mean: 15.743 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0.08 Å2
2---0.15 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.1→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 36 395 2458
Biso mean--15.75 33.86 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192238
X-RAY DIFFRACTIONr_bond_other_d0.0010.022081
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9573069
X-RAY DIFFRACTIONr_angle_other_deg0.78734841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19324.951103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73915368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.683157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
X-RAY DIFFRACTIONr_mcbond_it1.1961.2481080
X-RAY DIFFRACTIONr_mcbond_other1.1951.2451079
X-RAY DIFFRACTIONr_mcangle_it1.6781.8841361
X-RAY DIFFRACTIONr_rigid_bond_restr1.07934319
X-RAY DIFFRACTIONr_sphericity_free37.448581
X-RAY DIFFRACTIONr_sphericity_bonded11.08154552
LS refinement shellResolution: 1.102→1.131 Å /
RfactorNum. reflection
Rfree0.309 70
Rwork0.294 1275

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