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- PDB-3ffp: X ray structure of the complex between carbonic anhydrase II and ... -

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Basic information

Entry
Database: PDB / ID: 3ffp
TitleX ray structure of the complex between carbonic anhydrase II and LC inhibitors
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase / 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
BENZOIC ACID / : / Chem-LC1 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsTemperini, C. / Crocetti, L. / Scozzafava, A. / Supuran, C.T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: A thiabendazole sulfonamide shows potent inhibitory activity against mammalian and nematode alpha-carbonic anhydrases
Authors: Crocetti, L. / Maresca, A. / Temperini, C. / Hall, R.A. / Scozzafava, A. / Muhlschlegel, F.A. / Supuran, C.T.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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
X: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9585
Polymers29,2891
Non-polymers6684
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 41.430, 72.240
Angle α, β, γ (deg.)90.00, 104.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules X

#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: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 197 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-LC1 / 2-(1,3-thiazol-4-yl)-1H-benzimidazole-5-sulfonamide


Mass: 280.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N4O2S2
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE GAP IS IN THE SEQUENCE NUMBERING AS THE STARTING MODEL 1CA2.

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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: 41.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM Tris-HCl PH 7.7-7.8, 2mM sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
PH range: 7.7-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCED ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Sep 9, 2008
RadiationMonochromator: capillary / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→70 Å / Num. all: 22284 / Num. obs: 22187 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.055 / Net I/σ(I): 20.9
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.08 / Num. unique all: 2225 / Rsym value: 0.315 / % possible all: 100

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Processing

Software
NameVersionClassification
CrysalisProOxford Diffraction2006data collection
AMoREphasing
REFMAC5.2.0019refinement
CrysalisProOxford Diffraction2006data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA2

1ca2


Resolution: 1.81→11.83 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 2.936 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24018 1141 5.1 %RANDOM
Rwork0.1868 ---
obs0.18948 21415 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.02 Å2
2---0.05 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.81→11.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 29 193 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222146
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9622920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0224.74799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40515352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.764157
X-RAY DIFFRACTIONr_chiral_restr0.2950.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021661
X-RAY DIFFRACTIONr_nbd_refined0.2180.21029
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2179
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.216
X-RAY DIFFRACTIONr_mcbond_it0.9011.51326
X-RAY DIFFRACTIONr_mcangle_it1.40122076
X-RAY DIFFRACTIONr_scbond_it2.2613973
X-RAY DIFFRACTIONr_scangle_it3.3434.5840
LS refinement shellResolution: 1.81→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 90 -
Rwork0.219 1572 -
obs--100 %

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