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- PDB-5nxp: Carbonic Anhydrase II Inhibitor RA7 -

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Basic information

Entry
Database: PDB / ID: 5nxp
TitleCarbonic Anhydrase II Inhibitor RA7
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
Chem-9DH / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 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 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 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 1.2Jan 17, 2024Group: 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
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)29,4563
Polymers29,0711
Non-polymers3852
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.911, 41.040, 71.519
Angle α, β, γ (deg.)90.000, 104.310, 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-9DH / 2-[methyl(phenyl)amino]-~{N}-(4-sulfamoylphenyl)ethanamide


Mass: 319.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.05 Å3/Da / Density % sol: 40 %
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: 1.25→40.61 Å / Num. obs: 61012 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 2.064 % / Biso Wilson estimate: 18.262 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.054 / Χ2: 1.053 / Net I/σ(I): 9.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.25-1.321.8650.2482.2194780.8770.32590.1
1.32-1.422.0880.1823.2895800.9370.23596.6
1.42-1.532.0730.134.8788770.9640.16896.1
1.53-1.672.1160.0957.3681330.980.12295.3
1.67-1.872.0930.06510.9272780.990.08394.6
1.87-2.162.1050.04716.2562350.9940.06191.4
2.16-2.642.1280.0420.3852800.9950.05190.9
2.64-3.732.0920.03223.9839580.9970.04187.9
3.73-40.612.1630.02926.4921930.9970.03785.4

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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: 1.25→40.61 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.756 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.044
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1623 1001 1.6 %RANDOM
Rwork0.1282 ---
obs0.1287 60006 93.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.87 Å2 / Biso mean: 17.478 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.09 Å2
2---0.92 Å20 Å2
3---0.65 Å2
Refinement stepCycle: final / Resolution: 1.25→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 36 285 2340
Biso mean--16.6 32.12 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192426
X-RAY DIFFRACTIONr_bond_other_d0.0040.022189
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9483348
X-RAY DIFFRACTIONr_angle_other_deg1.1663.0045076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7924.825114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24815374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.519158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212862
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02588
X-RAY DIFFRACTIONr_rigid_bond_restr4.20734615
X-RAY DIFFRACTIONr_sphericity_free29.887567
X-RAY DIFFRACTIONr_sphericity_bonded9.57454738
LS refinement shellResolution: 1.249→1.281 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 65 -
Rwork0.227 3923 -
all-3988 -
obs--83.19 %

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