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- PDB-6xxt: The crystal structure of hCA II in complex with a 4-(4-aroylpiper... -

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Basic information

Entry
Database: PDB / ID: 6xxt
TitleThe crystal structure of hCA II in complex with a 4-(4-aroylpiperazine-1-carbonyl)benzenesulfonamide 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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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
Chem-O42 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsDi Fiore, A. / De Simone, G.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Looking toward the Rim of the Active Site Cavity of Druggable Human Carbonic Anhydrase Isoforms.
Authors: Mancuso, F. / Di Fiore, A. / De Luca, L. / Angeli, A. / Monti, S.M. / De Simone, G. / Supuran, C.T. / Gitto, R.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0084
Polymers29,4771
Non-polymers5313
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-7 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.333, 41.455, 72.131
Angle α, β, γ (deg.)90.000, 104.260, 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: 29477.307 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) / 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-O42 / 4-[4-(phenylcarbonyl)piperazin-1-yl]carbonylbenzenesulfonamide


Mass: 373.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 40.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.2 M sodium citrate 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 112517 / % possible obs: 99.2 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Rrim(I) all: 0.078 / Χ2: 1.051 / Net I/σ(I): 12.8 / Num. measured all: 652807
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.05-1.073.90.27749020.9010.1590.3230.96886.9
1.07-1.094.40.25956800.9260.1390.2961.01100
1.09-1.114.80.24456400.9410.1240.2761.057100
1.11-1.135.20.22356060.9570.1060.2481.095100
1.13-1.165.20.20155730.9630.0940.2221.09498.7
1.16-1.185.60.19456570.9670.0880.2141.09399.8
1.18-1.215.80.18356620.970.0830.2021.07100
1.21-1.245.90.17256130.9750.0760.1891.102100
1.24-1.286.10.16156690.9780.070.1761.066100
1.28-1.326.20.14756160.9790.0630.161.03199.1
1.32-1.376.30.1456480.9830.060.1521.076100
1.37-1.4360.12656470.9830.0560.1381.017100
1.43-1.496.30.11656740.9850.050.1271.056100
1.49-1.576.20.10556510.9880.0450.1140.9999.3
1.57-1.676.50.09656450.990.0410.1051.048100
1.67-1.86.10.08556960.990.0380.0931.038100
1.8-1.986.30.07556960.9930.0330.0821.068100
1.98-2.266.40.06556640.9950.0270.071.07499.4
2.26-2.856.40.05857370.9950.0250.0641.05100
2.85-506.40.05458410.9960.0230.0590.9999.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2

1ca2


Resolution: 1.05→35.68 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.645 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1455 1144 1 %RANDOM
Rwork0.1348 ---
obs0.1349 111103 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.46 Å2 / Biso mean: 10.499 Å2 / Biso min: 3.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å2-0.44 Å2
2--1.06 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 1.05→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 59 271 2397
Biso mean--12.86 21.37 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132262
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172015
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.623087
X-RAY DIFFRACTIONr_angle_other_deg1.4561.5734717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9425277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08223.796108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12415363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.078157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02470
X-RAY DIFFRACTIONr_rigid_bond_restr3.04334277
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 68 -
Rwork0.186 7613 -
all-7681 -
obs--92.2 %

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