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- PDB-7suy: Carbonic Anhydrase IX-mimic Complexed with 2-((3-Aminopropyl)(phe... -

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Basic information

Entry
Database: PDB / ID: 7suy
TitleCarbonic Anhydrase IX-mimic Complexed with 2-((3-Aminopropyl)(phenethyl)amino)-N-(4-fluorobenzyl)-N-(4-sulfamoylphenethyl)acetamide
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Lyase/Inhibitor / Inhibitor / Carbonic Anhydrase / Lyase-Inhibitor complex
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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / 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-C97 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.405 Å
AuthorsCombs, J.E. / McKenna, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Enzyme Inhib Med Chem / Year: 2022
Title: The three-tails approach as a new strategy to improve selectivity of action of sulphonamide inhibitors against tumour-associated carbonic anhydrase IX and XII.
Authors: Bonardi, A. / Bua, S. / Combs, J. / Lomelino, C. / Andring, J. / Osman, S.M. / Toti, A. / Di Cesare Mannelli, L. / Gratteri, P. / Ghelardini, C. / McKenna, R. / Nocentini, A. / Supuran, C.T.
History
DepositionNov 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)29,3694
Polymers28,8441
Non-polymers5253
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.959, 41.524, 71.707
Angle α, β, γ (deg.)90.000, 103.800, 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: 28844.465 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-C97 / N-[(furan-2-yl)methyl]-N-[2-(4-sulfamoylphenyl)ethyl]glycinamide


Mass: 337.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM tris base

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.405→32 Å / Num. obs: 46321 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.027 / Rrim(I) all: 0.05 / Net I/σ(I): 18.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.405-1.432.90.529639022220.7040.3630.6452.294.2
7.57-323.20.02110323260.9990.0130.02556.797.1

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zao

4zao


Resolution: 1.405→24.464 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1873 2262 4.89 %
Rwork0.1653 44037 -
obs0.1664 46299 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.58 Å2 / Biso mean: 19.3444 Å2 / Biso min: 6.08 Å2
Refinement stepCycle: final / Resolution: 1.405→24.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 51 198 2291
Biso mean--28.08 24.47 -
Num. residues----257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4053-1.43580.28041360.2577262094
1.4358-1.46920.25741340.2217264897
1.4692-1.50590.211340.1977272197
1.5059-1.54670.23181590.1908269898
1.5467-1.59220.2031300.1826273798
1.5922-1.64350.18051200.1717275599
1.6435-1.70230.20541520.1697272599
1.7023-1.77040.18731420.1633277699
1.7704-1.85090.20381790.1615272799
1.8509-1.94850.17451390.1658276599
1.9485-2.07050.20821290.1621279799
2.0705-2.23030.15921170.16032811100
2.2303-2.45450.17981570.15992798100
2.4545-2.80930.20181570.16822766100
2.8093-3.53770.18151250.1662825100
3.5377-24.4640.15531520.1435286899
Refinement TLS params.Method: refined / Origin x: -30.0908 Å / Origin y: -1.5986 Å / Origin z: 16.033 Å
111213212223313233
T0.0106 Å2-0.0009 Å20.0027 Å2-0.0077 Å20.002 Å2--0.0108 Å2
L0.3526 °2-0.0441 °20.121 °2-0.2052 °2-0.0951 °2--0.3192 °2
S-0.0168 Å °0.0177 Å °0.0226 Å °-0.0011 Å °0.0276 Å °0.0001 Å °0.0055 Å °0.0125 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allA301 - 401
3X-RAY DIFFRACTION1allB262
4X-RAY DIFFRACTION1allD1 - 206

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