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- PDB-7suw: Carbonic Anhydrase IX-mimic with 2-((3-Aminopropyl)(phenethyl)ami... -

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Basic information

Entry
Database: PDB / ID: 7suw
TitleCarbonic Anhydrase IX-mimic with 2-((3-Aminopropyl)(phenethyl)amino)-N-(furan-2-ylmethyl)-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 / positive regulation of synaptic transmission, GABAergic / 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 / 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-U77 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.456 Å
AuthorsMcKenna, R. / Combs, J.E.
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)29,5464
Polymers28,8441
Non-polymers7013
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.127, 41.737, 71.906
Angle α, β, γ (deg.)90.000, 103.860, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-U77 / N-(2-{[(furan-2-yl)methyl][2-(4-sulfamoylphenyl)ethyl]amino}-2-oxoethyl)-N-(2-phenylethyl)-beta-alanine


Mass: 513.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H31N3O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.13 Å3/Da / Density % sol: 42.19 %
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 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.45→34.91 Å / Num. obs: 40634 / % possible obs: 95.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.022 / Rrim(I) all: 0.042 / Net I/σ(I): 20.8
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
1.46-1.483.30.478647019340.7920.30.5662.689.4
7.84-34.913.10.0179162930.9990.010.0263.596.2

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Processing

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

4zao


Resolution: 1.456→22.698 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 2004 4.93 %
Rwork0.1614 38605 -
obs0.1628 40609 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.35 Å2 / Biso mean: 24.3086 Å2 / Biso min: 9.25 Å2
Refinement stepCycle: final / Resolution: 1.456→22.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 75 185 2302
Biso mean--39.7 27.78 -
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 (%)
1.4561-1.49250.26981300.2366261190
1.4925-1.53290.25481480.2109265093
1.5329-1.5780.23181600.1919266393
1.578-1.62890.20991480.1787270494
1.6289-1.68710.17821300.1696275695
1.6871-1.75460.20321440.1643275495
1.7546-1.83440.17461450.1671274395
1.8344-1.93110.19311470.1717274495
1.9311-2.0520.20861250.1614277595
2.052-2.21030.19371350.1642278096
2.2103-2.43250.19011430.1619281697
2.4325-2.7840.17491510.1638284097
2.784-3.50540.18331210.1603287997
3.5054-22.6980.18081770.1385289097
Refinement TLS params.Method: refined / Origin x: -30.276 Å / Origin y: -1.5585 Å / Origin z: 16.0997 Å
111213212223313233
T0.045 Å2-0.002 Å2-0.0004 Å2-0.0427 Å20.0041 Å2--0.0467 Å2
L0.35 °2-0.0361 °2-0.0466 °2-0.2627 °2-0.1528 °2--0.3225 °2
S-0.0098 Å °0.003 Å °0.0372 Å °-0.0173 Å °0.0286 Å °-0.0051 Å °0.0212 Å °0.003 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allB262
4X-RAY DIFFRACTION1allD1 - 192
5X-RAY DIFFRACTION1allC1

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