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- PDB-7ntb: Crystal structure of human carbonic anhydrase with a benzophenone... -

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Basic information

Entry
Database: PDB / ID: 7ntb
TitleCrystal structure of human carbonic anhydrase with a benzophenone-derivative
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Protein-inhibitor adduct
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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
MERCURIBENZOIC ACID / Chem-URH / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsDi Fiore, A. / De Simone, G.
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Interaction Studies between Carbonic Anhydrase and a Sulfonamide Inhibitor by Experimental and Theoretical Approaches
Authors: Pagnozzi, D. / Pala, N. / Biosa, G. / Dallocchio, R. / Dessi, A. / Singh, P.K. / Rogolino, D. / Di Fiore, A. / De Simone, G. / Supuran, C.T. / Sechi, M.
History
DepositionMar 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9394
Polymers29,1581
Non-polymers7823
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint3 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.140, 41.310, 72.100
Angle α, β, γ (deg.)90.000, 104.390, 90.000
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-URH / ~{N}-[[4-(phenylcarbonyl)phenyl]methyl]-4-sulfamoyl-benzamide


Mass: 394.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


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


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.6 M ammonium sulphate, 0.3 M sodium chloride, 0.1 M Tris-HCl, pH 8.5, 5 mM 4-(hydroxymercurybenzoate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 25551 / % possible obs: 95.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Χ2: 1.073 / Net I/σ(I): 39.1 / Num. measured all: 96154
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.7-1.762.60.09522971.081186.5
1.76-1.832.70.09223391.048189.2
1.83-1.912.80.08824481.038191.9
1.91-2.022.90.08224981.039194.5
2.02-2.143.10.08325761.116197.9
2.14-2.313.70.08426611.1481100
2.31-2.5440.08326501.068199.8
2.54-2.94.60.08826691.165199.9
2.9-3.665.40.08626751.022199.9
3.66-205.40.08227381.022199.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2

1ca2


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2168 1227 4.6 %
Rwork0.1726 24165 -
obs-25392 95.1 %
Solvent computationBsol: 52.7978 Å2
Displacement parametersBiso max: 60.55 Å2 / Biso mean: 12.3701 Å2 / Biso min: 1.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.955 Å20 Å2-0.678 Å2
2--0.521 Å20 Å2
3----1.476 Å2
Refinement stepCycle: final / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 39 299 2396
Biso mean--12.71 23.38 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.521
X-RAY DIFFRACTIONc_mcbond_it1.1841.5
X-RAY DIFFRACTIONc_scbond_it1.9192
X-RAY DIFFRACTIONc_mcangle_it1.7442
X-RAY DIFFRACTIONc_scangle_it2.8052.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.760.2397970.17972092218982.7
1.76-1.830.24521090.18032230233988.6
1.83-1.910.22351330.16412266239990.6
1.91-2.020.22051110.1652397250893.9
2.02-2.140.24791320.17852433256597.2
2.14-2.310.20411430.16512517266099.7
2.31-2.540.22421200.17772520264099.5
2.54-2.90.21281300.18512536266699.7
2.9-3.660.20661200.172567268799.9
3.66-200.2011320.16762607273999.1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep2.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6gliceroloCSD.param
X-RAY DIFFRACTION7dfc2.par

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