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- PDB-5nya: Carbonic Anhydrase II Inhibitor RA13 -

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Basic information

Entry
Database: PDB / ID: 5nya
TitleCarbonic Anhydrase II Inhibitor RA13
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic Anhydrase II / CA 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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / 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 / cytoplasm / cytosol
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
benzenesulfonamide / GLUTARIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsBrynda, J. / Rezacova, P. / Horejsi, M. / Fanfrlik, J.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Czech Science FoundationGA15-05677S Czech Republic
IMG of the Czech Academy of SciencesRVO 61388963 Czech Republic
IOCB of the Czech Academy of SciencesRVO 68378050 Czech Republic
Ministry of EducationLO1304 Czech Republic
CitationJournal: Chemphyschem / Year: 2018
Title: Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes.
Authors: Pecina, A. / Brynda, J. / Vrzal, L. / Gnanasekaran, R. / Horejsi, M. / Eyrilmez, S.M. / Rezac, J. / Lepsik, M. / Rezacova, P. / Hobza, P. / Majer, P. / Veverka, V. / Fanfrlik, J.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)29,2874
Polymers28,9331
Non-polymers3553
Water5,855325
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.227, 41.209, 72.152
Angle α, β, γ (deg.)90.000, 104.290, 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: 28932.641 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-FB2 / benzenesulfonamide


Mass: 157.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO2S
#4: Chemical ChemComp-GUA / GLUTARIC ACID


Mass: 132.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 50 mM Tris 1.6 M Natrium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.2→40.92 Å / Num. obs: 68565 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 3.79 % / Biso Wilson estimate: 14.621 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.068 / Χ2: 0.971 / Net I/σ(I): 12.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.272.8040.2753.2167550.9020.33655.7
1.27-1.363.4530.2124.8199720.9430.24987.1
1.36-1.474.0550.1636.88106250.9710.18999.9
1.47-1.614.0030.1129.8697900.9860.12999.9
1.61-1.83.990.08313.3688610.9910.09699.9
1.8-2.084.0740.06118.5578490.9950.0799.8
2.08-2.543.9180.05122.666350.9950.05999.5
2.54-3.583.8490.04625.5351580.9960.05399.2
3.58-40.923.7690.04327.6629190.9960.04999.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefmac_5.8.0103refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PO6

3po6


Resolution: 1.2→40.92 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.09 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.033
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1377 1002 1.5 %RANDOM
Rwork0.117 ---
obs0.1173 67563 90.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.05 Å2 / Biso mean: 14.578 Å2 / Biso min: 5.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.26 Å2
2---0.32 Å20 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 1.2→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 29 337 2389
Biso mean--9.98 26.76 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192312
X-RAY DIFFRACTIONr_bond_other_d0.0030.022116
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9523178
X-RAY DIFFRACTIONr_angle_other_deg1.0893.0014927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0315310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14324.865111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39115374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.697158
X-RAY DIFFRACTIONr_chiral_restr0.1110.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212703
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02539
X-RAY DIFFRACTIONr_rigid_bond_restr3.37832286
X-RAY DIFFRACTIONr_sphericity_free22.007559
X-RAY DIFFRACTIONr_sphericity_bonded11.54152449
LS refinement shellResolution: 1.199→1.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 39 -
Rwork0.173 2623 -
all-2662 -
obs--48.05 %

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