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- PDB-7nc4: Crystal structure of human carbonic anhydrase VII (hCA VII) in co... -

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Basic information

Entry
Database: PDB / ID: 7nc4
TitleCrystal structure of human carbonic anhydrase VII (hCA VII) in complex with a 4-(4-aroylpiperazine-1-carbonyl)benzenesulfonamide derivative.
ComponentsCarbonic anhydrase 7
KeywordsLYASE / Protein-inhibitor adduct
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding ...positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase VII / 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-U7Z / Carbonic anhydrase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsDi Fiore, A. / De Simone, G.
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Design, synthesis and biochemical evaluation of novel carbonic anhydrase inhibitors triggered by structural knowledge on hCA VII.
Authors: Mancuso, F. / Di Fiore, A. / De Luca, L. / Angeli, A. / De Simone, G. / Supuran, C.T. / Gitto, R.
History
DepositionJan 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
A: Carbonic anhydrase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5835
Polymers30,9261
Non-polymers6574
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-5 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.120, 89.370, 44.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Carbonic anhydrase 7 / Carbonate dehydratase VII / Carbonic anhydrase VII / CA-VII


Mass: 30925.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43166, 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-U7Z / 4-[4-(2-chlorophenyl)carbonylpiperazin-1-yl]carbonylbenzenesulfonamide / 4-(4-aroylpiperazine-1-carbonyl)benzenesulfonamide derivative


Mass: 407.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18ClN3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 0.2 M Sodium Acetate, 0.1 M Tris-HCl pH 8.5

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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: Oct 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 35392 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.017 / Rrim(I) all: 0.059 / Χ2: 1.059 / Net I/σ(I): 13.2 / Num. measured all: 427051
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6311.50.63817310.8920.1950.6681.07299.9
1.63-1.6611.90.5717450.9050.1710.5961.085100
1.66-1.6911.90.47617370.9360.1430.4981.07399.9
1.69-1.7211.60.39417370.9580.120.4121.104100
1.72-1.7611.40.32717510.9710.1010.3431.11199.9
1.76-1.811.90.27117360.9810.0820.2831.07100
1.8-1.8511.80.22417530.9860.0680.2351.08100
1.85-1.911.50.19117400.9880.0580.21.062100
1.9-1.9512.40.16117470.9920.0470.1671.072100
1.95-2.0212.30.13817420.9930.0410.1441.057100
2.02-2.09120.11717730.9950.0350.1221.079100
2.09-2.1711.70.10317450.9960.0310.1071.007100
2.17-2.2712.40.09217690.9960.0270.0961.08100
2.27-2.3912.30.08217590.9970.0240.0851.04100
2.39-2.5413.20.07617720.9980.0220.0791.007100
2.54-2.7412.80.06517990.9980.0190.0681.037100
2.74-3.0112.40.05417820.9980.0160.0561.093100
3.01-3.4512.30.04518080.9990.0130.0470.985100
3.45-4.3412.40.03618230.9990.0110.0381.015100
4.34-5011.50.03219430.9990.010.0331.07999.9

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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: 6G4T

6g4t


Resolution: 1.6→44.1 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.214 1044 3 %
Rwork0.1959 33630 -
obs-34674 98.4 %
Solvent computationBsol: 42.2493 Å2
Displacement parametersBiso max: 56.91 Å2 / Biso mean: 24.712 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.553 Å20 Å20 Å2
2--3.729 Å20 Å2
3----1.176 Å2
Refinement stepCycle: final / Resolution: 1.6→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 40 116 2211
Biso mean--34.69 33.02 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.527
X-RAY DIFFRACTIONc_mcbond_it1.3731.5
X-RAY DIFFRACTIONc_scbond_it2.1082
X-RAY DIFFRACTIONc_mcangle_it2.2352
X-RAY DIFFRACTIONc_scangle_it3.1242.5
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 (%)
1.6-1.660.3159910.28213163325493.6
1.66-1.720.28841030.24933215331896
1.72-1.80.23381000.2113274337497.3
1.8-1.90.21321020.20023337343998.5
1.9-2.020.19811250.1893314343999.3
2.02-2.170.21871020.19783394349699.7
2.17-2.390.20411060.19963405351199.9
2.39-2.740.25141030.200334393542100
2.74-3.450.19821050.194734663571100
3.45-44.10.19591070.180836233730100
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.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 DIFFRACTION7gitto3.param

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