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- PDB-6ugr: Human Carbonic Anhydrase 2 complexed with SB4-208 -

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Basic information

Entry
Database: PDB / ID: 6ugr
TitleHuman Carbonic Anhydrase 2 complexed with SB4-208
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / cyclical sulfonamide / inhibitor / LYASE / LYASE-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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / 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 / cytoplasm / cytosol
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-Q71 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.307 Å
AuthorsMurray, A.B. / Lomelino, C.L. / McKenna, R.
CitationJournal: J.Med.Chem. / Year: 2020
Title: "A Sweet Combination": Developing Saccharin and Acesulfame K Structures for Selectively Targeting the Tumor-Associated Carbonic Anhydrases IX and XII.
Authors: Bua, S. / Lomelino, C. / Murray, A.B. / Osman, S.M. / ALOthman, Z.A. / Bozdag, M. / Abdel-Aziz, H.A. / Eldehna, W.M. / McKenna, R. / Nocentini, A. / Supuran, C.T.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2143
Polymers28,9331
Non-polymers2822
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.279, 41.279, 71.939
Angle α, β, γ (deg.)90.000, 104.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2


Mass: 28932.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00918
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-Q71 / 7-fluoro-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione


Mass: 216.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 41.54 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 1.6 M sodium citrate, 50 mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.307→32.09 Å / Num. obs: 56762 / % possible obs: 97 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Net I/σ(I): 24.1
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
1.31-1.335.60.5271494926660.8730.2390.581392.1
7.16-32.096.40.02524893870.9990.010.02765.299

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.307→32.088 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.65
RfactorNum. reflection% reflection
Rfree0.1651 2792 4.92 %
Rwork0.1513 --
obs0.152 56756 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.34 Å2 / Biso mean: 18.0456 Å2 / Biso min: 6.39 Å2
Refinement stepCycle: final / Resolution: 1.307→32.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 19 216 2284
Biso mean--11.44 24.65 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082139
X-RAY DIFFRACTIONf_angle_d1.1222909
X-RAY DIFFRACTIONf_chiral_restr0.084301
X-RAY DIFFRACTIONf_plane_restr0.01377
X-RAY DIFFRACTIONf_dihedral_angle_d14.977780
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.307-1.32940.21711380.2282255792
1.3294-1.35360.20191690.2067258296
1.3536-1.37960.22311320.1878262795
1.3796-1.40780.19841230.1815268796
1.4078-1.43840.196990.1781266595
1.4384-1.47180.18231110.1614267996
1.4718-1.50860.191340.1545267596
1.5086-1.54940.17981460.15263496
1.5494-1.5950.13581420.1472269496
1.595-1.64650.15581410.1447265797
1.6465-1.70530.16821370.1489268897
1.7053-1.77360.16171470.1458269498
1.7736-1.85430.17731540.1451271098
1.8543-1.95210.14871310.1451272198
1.9521-2.07440.16211510.1395273198
2.0744-2.23450.13781550.1385274199
2.2345-2.45930.17281270.1428277199
2.4593-2.8150.15911500.1575278299
2.815-3.54580.17261370.16280299
3.5458-32.0880.1571680.14042867100
Refinement TLS params.Method: refined / Origin x: 11.6147 Å / Origin y: -1.8147 Å / Origin z: 16.0102 Å
111213212223313233
T0.0707 Å2-0.0035 Å20.0007 Å2-0.067 Å20.0018 Å2--0.0717 Å2
L0.5139 °2-0.0576 °2-0.0068 °2-0.3967 °2-0.0183 °2--0.4777 °2
S-0.0103 Å °-0.0053 Å °0.0071 Å °-0.0237 Å °0.0097 Å °-0.0011 Å °0.0112 Å °0.0075 Å °-0.0081 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 222
4X-RAY DIFFRACTION1allC1

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