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- PDB-7sv8: Carbonic Anhydrase IX-mimic Complexed with 3-((2-((Furan-2-ylmeth... -

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Basic information

Entry
Database: PDB / ID: 7sv8
TitleCarbonic Anhydrase IX-mimic Complexed with 3-((2-((Furan-2-ylmethyl)(4-sulfamoylphenethyl)amino)-2-oxoethyl)(phenethyl)amino)propanoic acid
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...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 / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / 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-U7J / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.388 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)29,6064
Polymers28,8441
Non-polymers7613
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.816, 41.575, 72.117
Angle α, β, γ (deg.)90.000, 103.760, 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-U7J / N-(2-{[(naphthalen-2-yl)methyl][2-(4-sulfamoylphenyl)ethyl]amino}-2-oxoethyl)-N-(2-phenylethyl)-beta-alanine


Mass: 573.702 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H35N3O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.388→35.75 Å / Num. obs: 46399 / % possible obs: 95.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.019 / Rrim(I) all: 0.035 / Net I/σ(I): 20.3
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
1.388-1.412.40.277353014990.870.2140.3532.762.6
7.6-35.753.30.01510713220.9990.0090.01852.197.3

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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: 1.388→35.024 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 2280 4.92 %
Rwork0.154 44094 -
obs0.1551 46374 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.91 Å2 / Biso mean: 22.4309 Å2 / Biso min: 8.84 Å2
Refinement stepCycle: final / Resolution: 1.388→35.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 84 182 2308
Biso mean--40.13 27.5 -
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 (%)
1.3881-1.41830.2534950.2087190567
1.4183-1.45130.20141280.1938268993
1.4513-1.48760.21711470.1783286398
1.4876-1.52780.19951350.1767281498
1.5278-1.57270.20131550.1648282698
1.5727-1.62350.20651670.1658276897
1.6235-1.68150.17571340.1678279396
1.6815-1.74880.17591530.1563285499
1.7488-1.82840.1991560.1565286899
1.8284-1.92480.17271370.163274195
1.9248-2.04540.18271370.1489275995
2.0454-2.20330.17021480.1478286798
2.2033-2.4250.17081530.1495280197
2.425-2.77580.16131540.1545279296
2.7758-3.49670.19031380.1539286597
3.4967-35.0240.15811430.141288996
Refinement TLS params.Method: refined / Origin x: -29.9165 Å / Origin y: -1.4091 Å / Origin z: 16.1135 Å
111213212223313233
T0.039 Å20.0011 Å20.0015 Å2-0.0374 Å20.0004 Å2--0.039 Å2
L0.3871 °20.0011 °20.0479 °2-0.2861 °2-0.0692 °2--0.3377 °2
S-0.0172 Å °-0.0007 Å °0.0226 Å °-0.015 Å °0.0256 Å °-0.0046 Å °0.0036 Å °0.0041 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 - 186
5X-RAY DIFFRACTION1allC1

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