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- PDB-3bet: Crystal structure of the human carbonic anhydrase II in complex w... -

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Basic information

Entry
Database: PDB / ID: 3bet
TitleCrystal structure of the human carbonic anhydrase II in complex with STX 641 at 1.85 angstroms resolution
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Protein-inhibitor complex / Disease mutation / Metal-binding
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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-CTF / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsDi Fiore, A. / De Simone, G.
Citation
Journal: J.Med.Chem. / Year: 2008
Title: Structure-activity relationships of C-17 cyano-substituted estratrienes as anticancer agents
Authors: Leese, M.P. / Jourdan, F.L. / Gaukroger, K. / Mahon, M.F. / Newman, S.P. / Foster, P.A. / Stengel, C. / Regis-Lydi, S. / Ferrandis, E. / Di Fiore, A. / De Simone, G. / Supuran, C.T. / ...Authors: Leese, M.P. / Jourdan, F.L. / Gaukroger, K. / Mahon, M.F. / Newman, S.P. / Foster, P.A. / Stengel, C. / Regis-Lydi, S. / Ferrandis, E. / Di Fiore, A. / De Simone, G. / Supuran, C.T. / Purohit, A. / Reed, M.J. / Potter, B.V.
#1: Journal: Proteins / Year: 1988
Title: Refined structure of human carbonic anhydrase II at 2.0 A resolution
Authors: Eriksson, A.E. / Jones, T.A. / Liljas, A.
#2: Journal: J.Med.Chem. / Year: 2006
Title: 2-substituted estradiol bis-sulfamates, multitargeted antitumor agents: synthesis, in vitro SAR, protein crystallography, and in vivo activity
Authors: Leese, M.P. / Leblond, B. / Smith, A. / Newman, S.P. / Di Fiore, A. / De Simone, G. / Supuran, C.T. / Purohit, A. / Reed, M.J. / Potter, B.V.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)29,7204
Polymers29,1581
Non-polymers5623
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.17, 41.49, 71.58
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonic anhydrase II / Carbonate dehydratase II / CA-II / Carbonic anhydrase C


Mass: 29157.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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-CTF / (17beta)-17-(cyanomethyl)-2-methoxyestra-1(10),2,4-trien-3-yl sulfamate / 2-methoxy-17beta-cyanomethylestra-1,3,5,(10)-trien-3-O-sulfamate, 19-Norpregna-1,3,5(10)-triene-21-nitrile,3-[(aminosulfonyl)oxy]-2-methoxy


Mass: 404.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N2O4S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 292 / 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: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 2.8M ammonium sulphate, 0.3M sodium chloride, 0.1M TRIS-HCl pH 8.4, 1mM dithiothreitol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 20038 / Num. obs: 20038 / % possible obs: 96.6 % / Redundancy: 3 % / Rsym value: 0.072 / Net I/σ(I): 15.2
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 4.51 / Num. unique all: 1833 / Rsym value: 0.237 / % possible all: 89.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1CA2

1ca2


Resolution: 1.85→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 952 -RANDOM
Rwork0.17 ---
all-20038 --
obs-19587 94.4 %-
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 35 292 2386
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4

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