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- PDB-3t5z: Crystal structure of the human carbonic anhydrase II in complex w... -

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Basic information

Entry
Database: PDB / ID: 3t5z
TitleCrystal structure of the human carbonic anhydrase II in complex with N-methoxy-benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Protein-inhibitor complex / 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 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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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
N-methoxybenzenesulfonamide / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsDi Fiore, A. / Maresca, A. / Alterio, V. / Supuran, C.T. / De Simone, G.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2011
Title: Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of N-substituted benzenesulfonamides to human isoform II.
Authors: Di Fiore, A. / Maresca, A. / Alterio, V. / Supuran, C.T. / De Simone, G.
#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: Chemmedchem / Year: 2009
Title: Thermodynamic optimisation in drug discovery: a case study using carbonic anhydrase inhibitors.
Authors: Scott, A.D. / Phillips, C. / Alex, A. / Flocco, M. / Bent, A. / Randall, A. / O'Brien, R. / Damian, L. / Jones, L.H.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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)29,7324
Polymers29,1581
Non-polymers5743
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.11, 41.32, 71.84
Angle α, β, γ (deg.)90.00, 104.32, 90.00
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: 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-B09 / N-methoxybenzenesulfonamide


Mass: 187.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO3S
#4: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.6 M ammonium sulfate, 0.3 M sodium chloride, 0.1 M Tris-HCl, pH 8.5, 5 mM 4-hydroxymercurybenzoate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN / Detector: CCD / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 28042 / Num. obs: 28042 / % possible obs: 96.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.03
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 13.45 / Num. unique all: 2511 / % possible all: 87.6

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1CA2

1ca2


Resolution: 1.65→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1354 4.7 %RANDOM
Rwork0.1792 26537 --
all-28042 --
obs-27891 96 %-
Solvent computationBsol: 43.3279 Å2
Displacement parametersBiso max: 52.48 Å2 / Biso mean: 13.6681 Å2 / Biso min: 2.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.091 Å20 Å2-0.306 Å2
2---0.197 Å20 Å2
3---1.288 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 23 356 2438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1141.5
X-RAY DIFFRACTIONc_scbond_it1.8352
X-RAY DIFFRACTIONc_mcangle_it1.6722
X-RAY DIFFRACTIONc_scangle_it2.6822.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4b09.par

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