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- PDB-8fqz: Carbonic Anhydrase II in complex with the alkyl urea 3j -

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Basic information

Entry
Database: PDB / ID: 8fqz
TitleCarbonic Anhydrase II in complex with the alkyl urea 3j
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Lyase / Inhibitor
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 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
Chem-N7S / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.467 Å
AuthorsCombs, J.C. / McKenna, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2023
Title: New Insights into Conformationally Restricted Carbonic Anhydrase Inhibitors.
Authors: Combs, J. / Bozdag, M. / Cravey, L.D. / Kota, A. / McKenna, R. / Angeli, A. / Carta, F. / Supuran, C.T.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)29,8145
Polymers29,2891
Non-polymers5254
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.277, 41.154, 71.914
Angle α, β, γ (deg.)90.00, 104.26, 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 / Production host: Escherichia coli (E. coli) / 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-N7S / 4-hydroxy-3-{[(4-hydroxybutyl)carbamoyl]amino}benzene-1-sulfonamide


Mass: 303.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris base

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.4→30.5 Å / Num. obs: 40672 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.6
Reflection shellResolution: 1.4→1.5 Å / Rmerge(I) obs: 0.57 / Num. unique obs: 12839

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.467→30.5 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1853 1944 4.78 %
Rwork0.1644 --
obs0.1654 40670 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.467→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 29 271 2349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122152
X-RAY DIFFRACTIONf_angle_d1.2162922
X-RAY DIFFRACTIONf_dihedral_angle_d13.761786
X-RAY DIFFRACTIONf_chiral_restr0.1301
X-RAY DIFFRACTIONf_plane_restr0.01380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4672-1.50390.45111210.44472646X-RAY DIFFRACTION95
1.5039-1.54450.32441420.31792716X-RAY DIFFRACTION98
1.5445-1.590.23971270.22072763X-RAY DIFFRACTION98
1.59-1.64130.20681290.18482738X-RAY DIFFRACTION98
1.6413-1.70.19921240.1762742X-RAY DIFFRACTION98
1.7-1.7680.19741290.16912781X-RAY DIFFRACTION99
1.768-1.84850.19781600.17492766X-RAY DIFFRACTION99
1.8485-1.94590.17681790.16212716X-RAY DIFFRACTION99
1.9459-2.06780.16551410.15352752X-RAY DIFFRACTION99
2.0678-2.22740.18451140.15272831X-RAY DIFFRACTION99
2.2274-2.45150.19081360.162795X-RAY DIFFRACTION100
2.4515-2.8060.17821440.16492813X-RAY DIFFRACTION100
2.806-3.53440.18131550.15082804X-RAY DIFFRACTION99
3.5344-30.50.15021430.13452863X-RAY DIFFRACTION99

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