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- PDB-5eij: Carbonic Anhydrase II in complex with Sulfonamide Inhibitor -

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Basic information

Entry
Database: PDB / ID: 5eij
TitleCarbonic Anhydrase II in complex with Sulfonamide Inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLyase/Lyase Inhibitor / sulfonamide / inhibitor / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...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 / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / 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
1-(3-iodanylphenyl)-3-(4-sulfamoylphenyl)thiourea / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsLomelino, C.L. / Mahon, B.P. / McKenna, R.
CitationJournal: Bioorg. Med. Chem. / Year: 2016
Title: Kinetic and X-ray crystallographic investigations on carbonic anhydrase isoforms I, II, IX and XII of a thioureido analog of SLC-0111.
Authors: Lomelino, C.L. / Mahon, B.P. / McKenna, R. / Carta, F. / Supuran, C.T.
History
DepositionOct 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7727
Polymers28,9331
Non-polymers8396
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.386, 41.663, 72.707
Angle α, β, γ (deg.)90.000, 104.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 28932.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 98 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5OT / 1-(3-iodanylphenyl)-3-(4-sulfamoylphenyl)thiourea


Mass: 433.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12IN3O2S2
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 1.6M sodium citrate, 50mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9782 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. obs: 15741 / % possible obs: 90.9 % / Redundancy: 2 % / Biso Wilson estimate: 14.42 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.049 / Rrim(I) all: 0.077 / Χ2: 3.844 / Net I/av σ(I): 26.354 / Net I/σ(I): 18.9 / Num. measured all: 32115
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.99-2.021.90.1147820.9650.0950.1492.3291.9
2.02-2.0620.1017480.9670.0830.1312.29188.2
2.06-2.120.1947800.5230.1660.2578.63991.4
2.1-2.1420.0887910.9780.0710.1132.61389.8
2.14-2.1920.0827600.9810.0660.1062.40690.7
2.19-2.2420.0827860.9750.0690.1082.82191.3
2.24-2.320.1067880.8710.0890.1394.97591.5
2.3-2.3620.0768000.9850.0610.0983.02692.3
2.36-2.4320.0647770.9890.0520.0832.56691.7
2.43-2.512.10.0668040.9860.0540.0852.61891.5
2.51-2.62.10.0638040.9880.0520.0822.83292
2.6-2.72.10.0718000.9840.0570.0913.62293.8
2.7-2.822.10.0577870.9880.0470.0743.14391.8
2.82-2.9720.0538060.9920.0430.0682.99192.4
2.97-3.162.10.0497820.9910.040.0643.27591
3.16-3.42.10.0467770.9930.0360.0583.71790.1
3.4-3.742.10.0538020.9780.0430.0695.89990.6
3.74-4.272.10.0458130.9930.0360.0584.93791.6
4.27-5.372.10.0477840.990.0380.0615.00389.3
5.37-2020.0627700.9820.0510.086.92784.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å18.58 Å
Translation6.05 Å18.58 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.99→20 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 801 5.09 %Random Selection
Rwork0.1586 14928 --
obs0.1617 15729 89.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.08 Å2 / Biso mean: 15.8026 Å2 / Biso min: 2.09 Å2
Refinement stepCycle: final / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 42 92 2183
Biso mean--25.29 17.98 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082153
X-RAY DIFFRACTIONf_angle_d1.172916
X-RAY DIFFRACTIONf_chiral_restr0.048300
X-RAY DIFFRACTIONf_plane_restr0.005374
X-RAY DIFFRACTIONf_dihedral_angle_d14.061782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.99-2.09930.25621190.1634231884
2.0993-2.26110.21291300.1604248891
2.2611-2.48820.25881420.1722253992
2.4882-2.84720.22011310.1749254892
2.8472-3.58290.22181370.1721251791
3.58290.18721420.1316251889
Refinement TLS params.Method: refined / Origin x: -9.4664 Å / Origin y: -1.7474 Å / Origin z: 16.1885 Å
111213212223313233
T0.021 Å2-0.0059 Å2-0.0002 Å2-0.0189 Å20.003 Å2--0.0261 Å2
L0.4596 °2-0.1391 °20.012 °2-0.3739 °2-0.0335 °2--0.514 °2
S0.0045 Å °-0.0092 Å °0.002 Å °-0.0142 Å °-0.0024 Å °0.0147 Å °0.0032 Å °0.0087 Å °0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allC2 - 40
4X-RAY DIFFRACTION1allC41 - 59
5X-RAY DIFFRACTION1allC60 - 67
6X-RAY DIFFRACTION1allC68 - 84
7X-RAY DIFFRACTION1allC85 - 94
8X-RAY DIFFRACTION1allD1
9X-RAY DIFFRACTION1allE1 - 2
10X-RAY DIFFRACTION1allF400
11X-RAY DIFFRACTION1allF402

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