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- PDB-3dcc: Use of Carbonic Anhydrase II, IX Active-Site Mimic, for the Purpo... -

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Basic information

Entry
Database: PDB / ID: 3dcc
TitleUse of Carbonic Anhydrase II, IX Active-Site Mimic, for the Purpose of Screening Inhibitors for Possible Anti-Cancer Properties
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic anhydrase II complex / CAIX mimic inhibitors / Acetylation / Cytoplasm / Disease mutation / Metal-binding / Polymorphism / Zinc
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-D9Z / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 1.6 Å
AuthorsGenis, C. / Sippel, K.H. / Case, N. / Govindasamy, L. / Agbandje-Mckenna, M. / Mckenna, R.
CitationJournal: Biochemistry / Year: 2009
Title: Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties
Authors: Genis, C. / Sippel, K.H. / Case, N. / Cao, W. / Avvaru, B.S. / Tartaglia, L.J. / Govindasamy, L. / Tu, C. / Agbandje-McKenna, M. / Silverman, D.N. / Rosser, C.J. / McKenna, R.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,6603
Polymers29,3191
Non-polymers3412
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.890, 41.900, 73.000
Angle α, β, γ (deg.)90.00, 104.61, 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 / CAC


Mass: 29319.086 Da / Num. of mol.: 1 / Mutation: A65S,N67Q
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-D9Z / 5-(2-chlorophenyl)-1,3,4-thiadiazole-2-sulfonamide


Mass: 275.735 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6ClN3O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.3M sodium citrate, 100mM Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 1, 2008 / Details: osmic mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 26650 / Num. obs: 26650 / % possible obs: 79.8 % / Redundancy: 2.1 % / Rsym value: 0.064
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.1 % / Num. unique all: 2547 / Rsym value: 0.297 / % possible all: 76.5

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB entry 1MOO

1moo


Resolution: 1.6→20 Å / Num. parameters: 9231 / Num. restraintsaints: 8948 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.206 --RANDOM
Rwork0.146 ---
all-26650 --
obs-26650 79.8 %-
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2215.5
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 17 180 2307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0293
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.079
X-RAY DIFFRACTIONs_approx_iso_adps0

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