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- PDB-5sz6: Carbonic anhydrase IX-mimic in complex with 4-(3-formylphenyl)-be... -

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Basic information

Entry
Database: PDB / ID: 5sz6
TitleCarbonic anhydrase IX-mimic in complex with 4-(3-formylphenyl)-benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLyase/Lyase Inhibitor / sulfonamide / inhibitor / zinc-binding / 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
4-(3-formylphenyl)-benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsBhatt, A. / Mahon, B.P. / Cornelio, B. / McKenna, R.
CitationJournal: Chembiochem / Year: 2017
Title: Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity.
Authors: Bhatt, A. / Mahon, B.P. / Cruzeiro, V.W. / Cornelio, B. / Laronze-Cochard, M. / Ceruso, M. / Sapi, J. / Rance, G.A. / Khlobystov, A.N. / Fontana, A. / Roitberg, A. / Supuran, C.T. / McKenna, R.
History
DepositionAug 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
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)29,4206
Polymers28,8441
Non-polymers5755
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.020, 41.474, 72.229
Angle α, β, γ (deg.)90.00, 103.77, 90.00
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: 28844.465 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, 369 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-72G / 4-(3-formylphenyl)-benzenesulfonamide / 3'-formyl[1,1'-biphenyl]-4-sulfonamide


Mass: 261.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO3S
#4: 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
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.6M Sodium Citrate, 50mM Tris pH 7.8 / PH range: 7.2-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.15→19.953 Å / Num. obs: 84634 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.112 / Net I/av σ(I): 11.992 / Net I/σ(I): 3.5
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 6 % / Rmerge(I) obs: 0.618 / CC1/2: 0.877 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.15→19.953 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1588 2010 2.37 %
Rwork0.1436 --
obs0.144 84634 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→19.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 33 364 2439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082166
X-RAY DIFFRACTIONf_angle_d1.3182947
X-RAY DIFFRACTIONf_dihedral_angle_d13.286790
X-RAY DIFFRACTIONf_chiral_restr0.077312
X-RAY DIFFRACTIONf_plane_restr0.007378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1498-1.17850.21171520.21635642X-RAY DIFFRACTION95
1.1785-1.21040.18711360.18655781X-RAY DIFFRACTION97
1.2104-1.2460.21651390.17825788X-RAY DIFFRACTION97
1.246-1.28620.18881480.17285838X-RAY DIFFRACTION98
1.2862-1.33220.19091380.16045884X-RAY DIFFRACTION98
1.3322-1.38550.16231350.16035876X-RAY DIFFRACTION98
1.3855-1.44850.15821450.14955897X-RAY DIFFRACTION99
1.4485-1.52490.15631480.14785966X-RAY DIFFRACTION100
1.5249-1.62040.1631350.1415976X-RAY DIFFRACTION100
1.6204-1.74540.15461480.14036014X-RAY DIFFRACTION100
1.7454-1.92090.13591440.13855967X-RAY DIFFRACTION100
1.9209-2.19860.13761480.13166047X-RAY DIFFRACTION100
2.1986-2.76880.16071490.13226033X-RAY DIFFRACTION100
2.7688-19.95630.15261450.13385915X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 12.0547 Å / Origin y: -1.6117 Å / Origin z: 16.0338 Å
111213212223313233
T0.0642 Å20.0012 Å20.0037 Å2-0.0622 Å20.0024 Å2--0.0637 Å2
L0.6116 °2-0.0108 °20.1646 °2-0.5215 °2-0.0596 °2--0.5226 °2
S-0.0113 Å °0.0083 Å °0.0323 Å °-0.025 Å °0.021 Å °-0.009 Å °0.0056 Å °0.016 Å °0.0544 Å °
Refinement TLS groupSelection details: all

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