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- PDB-5ny6: Carbonic Anhydrase II Inhibitor RA12 -

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Basic information

Entry
Database: PDB / ID: 5ny6
TitleCarbonic Anhydrase II Inhibitor RA12
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 / 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 / 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
Chem-9EB / Chem-R92 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 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 / Derived calculations / 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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)29,8464
Polymers29,0711
Non-polymers7753
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.013, 41.107, 72.077
Angle α, β, γ (deg.)90.000, 104.230, 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: 29070.785 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-9EB / 4-chloranyl-~{N}-[(1~{R})-1-(2-hydroxyphenyl)ethyl]-3-sulfamoyl-benzamide


Mass: 354.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15ClN2O4S
#4: Chemical ChemComp-R92 / 4-chloranyl-~{N}-[(1~{S})-1-(2-hydroxyphenyl)ethyl]-3-sulfamoyl-benzamide


Mass: 354.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15ClN2O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
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: 1.1→40.72 Å / Num. obs: 73966 / % possible obs: 76.4 % / Observed criterion σ(I): -3 / Redundancy: 4.04 % / Biso Wilson estimate: 13.078 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.052 / Χ2: 1.026 / Net I/σ(I): 16.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.172.3470.2662.8930330.8750.33819.4
1.17-1.252.8290.2174.0769690.9260.26747.6
1.25-1.353.5670.1656.11110700.9620.19481.5
1.35-1.484.4780.1289.29125840.9830.14599.9
1.48-1.654.4650.08713.79113850.9920.09999.9
1.65-1.94.4160.06219.85100540.9960.0799.8
1.9-2.334.3780.04428.9185160.9970.0599.8
2.33-3.294.3010.03735.5566210.9980.04299.7
3.29-40.724.0620.03141.2237340.9980.03699.2

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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: 1.1→40.72 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.885 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.037
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1544 999 1.4 %RANDOM
Rwork0.1392 ---
obs0.1394 72966 76.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.9 Å2 / Biso mean: 13.955 Å2 / Biso min: 3.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.05 Å2
2---0.33 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.1→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 70 314 2421
Biso mean--14.78 29.86 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192569
X-RAY DIFFRACTIONr_bond_other_d0.0050.022344
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9753526
X-RAY DIFFRACTIONr_angle_other_deg1.11535427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37924.833120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98115404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.504159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212995
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02619
X-RAY DIFFRACTIONr_rigid_bond_restr5.91931711
X-RAY DIFFRACTIONr_sphericity_free31.214560
X-RAY DIFFRACTIONr_sphericity_bonded12.38451936
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 11 -
Rwork0.22 838 -
all-849 -
obs--11.9 %

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