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- PDB-3l14: Human Carbonic Anhydrase II complexed with Althiazide -

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Basic information

Entry
Database: PDB / ID: 3l14
TitleHuman Carbonic Anhydrase II complexed with Althiazide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase II / althiazide / 6-chloro-3 / 4-dihydro-3-((2-propenylthio)methyl)-2H-1 / 2 / 4-benzothiadiazine-7-sulfonamide / 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
4-AMINO-6-CHLOROBENZENE-1,3-DISULFONAMIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.22 Å
AuthorsQuirit, J.G. / Robbins, A. / Genis, C. / Tu, C. / Silverman, D.N. / McKenna, R.
CitationJournal: To be Published
Title: The Promiscuous Nature of Althiazide in Adducts with CA II and CA IX Mimic
Authors: Quirit, J.G. / Robbins, A. / Rocca, J.R. / Johnson, J. / Genis, C. / Tu, C. / Silverman, D.N. / McKenna, R.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6403
Polymers29,2891
Non-polymers3512
Water5,603311
1
A: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2806
Polymers58,5782
Non-polymers7024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.158, 41.396, 72.391
Angle α, β, γ (deg.)90.00, 104.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29289.062 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) / Strain (production host): Bl21(de3)plyss / 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-I7B / 4-AMINO-6-CHLOROBENZENE-1,3-DISULFONAMIDE


Mass: 285.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8ClN3O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 50 mM Tris-HCl, 1.3 M Sodium Citrate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. all: 69912 / Num. obs: 65974 / % possible obs: 92.3 % / Redundancy: 5.3 % / Rsym value: 0.116
Reflection shellResolution: 1.22→1.24 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: NONE

Resolution: 1.22→20 Å / Num. parameters: 21487 / Num. restraintsaints: 27676 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 --RANDOM
Rwork0.1299 ---
obs-64630 91.3 %-
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 1880.5 / Occupancy sum non hydrogen: 2339.5
Refinement stepCycle: LAST / Resolution: 1.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 17 311 2377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0311
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.045
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.072

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