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- PDB-5wlv: Carbonic Anhydrase II in complex with aryloxy-2-hydroxypropylammi... -

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Basic information

Entry
Database: PDB / ID: 5wlv
TitleCarbonic Anhydrase II in complex with aryloxy-2-hydroxypropylammine sulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/INHIBITOR / carbonic anhydrase / beta adrenergic receptor / sulfonamide / aryloxy-2-hydroxypropylammine / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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-42G / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLomelino, C.L. / Andring, J.T. / McKenna, R.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of beta-Adrenergic Receptors Blocker-Carbonic Anhydrase Inhibitor Hybrids for Multitargeted Antiglaucoma Therapy.
Authors: Nocentini, A. / Ceruso, M. / Bua, S. / Lomelino, C.L. / Andring, J.T. / McKenna, R. / Lanzi, C. / Sgambellone, S. / Pecori, R. / Matucci, R. / Filippi, L. / Gratteri, P. / Carta, F. / ...Authors: Nocentini, A. / Ceruso, M. / Bua, S. / Lomelino, C.L. / Andring, J.T. / McKenna, R. / Lanzi, C. / Sgambellone, S. / Pecori, R. / Matucci, R. / Filippi, L. / Gratteri, P. / Carta, F. / Masini, E. / Selleri, S. / Supuran, C.T.
History
DepositionJul 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Oct 4, 2023Group: 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)30,0396
Polymers28,9331
Non-polymers1,1075
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-2 kcal/mol
Surface area11860 Å2
Unit cell
Length a, b, c (Å)42.598, 41.602, 72.480
Angle α, β, γ (deg.)90.000, 104.260, 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 / Fragment: UNP residues 4-260
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

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Non-polymers , 5 types, 239 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-42G / 4-{(2R)-2-hydroxy-3-[(propan-2-yl)amino]propoxy}-N-[2-(4-sulfamoylphenyl)ethyl]benzamide / aryloxy-2-hydroxypropylammine sulfonamide


Mass: 435.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 42.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M Sodium Citrate 50mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.39→30.8 Å / Num. obs: 69038 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.17 Å2 / Net I/σ(I): 21.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.4→30.8 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.72
RfactorNum. reflection% reflectionSelection details
Rfree0.1669 2811 4.07 %0.05
Rwork0.1446 ---
obs0.1455 69038 71.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.23 Å2 / Biso mean: 19.168 Å2 / Biso min: 8.87 Å2
Refinement stepCycle: final / Resolution: 1.4→30.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 71 234 2354
Biso mean--37.85 29.78 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062233
X-RAY DIFFRACTIONf_angle_d0.9393042
X-RAY DIFFRACTIONf_chiral_restr0.086309
X-RAY DIFFRACTIONf_plane_restr0.005396
X-RAY DIFFRACTIONf_dihedral_angle_d15.385816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3904-1.41440.25451030.22272164226746
1.4144-1.44010.2108800.20552276235649
1.4401-1.46780.22531070.1992371247850
1.4678-1.49770.2141090.1822324243351
1.4977-1.53030.2075870.17292429251651
1.5303-1.56590.17221070.1672391249852
1.5659-1.60510.19091060.16392521262754
1.6051-1.64840.17621130.15392756286959
1.6484-1.69690.18281270.15492979310664
1.6969-1.75170.15471310.14973232336369
1.7517-1.81430.20391540.14783442359674
1.8143-1.8870.17791610.14513627378878
1.887-1.97280.18781600.14023935409584
1.9728-2.07680.16691760.13744142431889
2.0768-2.20690.15571730.1414196436990
2.2069-2.37720.14981870.14524114430189
2.3772-2.61630.17261770.14994246442392
2.6163-2.99470.19021880.15354361454993
2.9947-3.77190.15551750.13274300447592
3.7719-30.75760.14051900.13074421461195
Refinement TLS params.Method: refined / Origin x: -9.773 Å / Origin y: -1.4371 Å / Origin z: 16.0202 Å
111213212223313233
T0.1012 Å2-0.01 Å20.0015 Å2-0.0998 Å20.0007 Å2--0.1053 Å2
L0.5339 °2-0.1262 °20.0467 °2-0.4424 °2-0.0651 °2--0.5131 °2
S-0.0027 Å °-0.0203 Å °0.0244 Å °-0.0191 Å °0.0103 Å °0.005 Å °0.0059 Å °0.0116 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allD2 - 185
4X-RAY DIFFRACTION1allD186 - 227
5X-RAY DIFFRACTION1allD228 - 235
6X-RAY DIFFRACTION1allD236 - 242
7X-RAY DIFFRACTION1allD243 - 249
8X-RAY DIFFRACTION1allC1 - 2
9X-RAY DIFFRACTION1allE1
10X-RAY DIFFRACTION1allF400

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