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- PDB-6ugz: Human Carbonic Anhydrase IX-mimic complexed with SB4-208 -

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Basic information

Entry
Database: PDB / ID: 6ugz
TitleHuman Carbonic Anhydrase IX-mimic complexed with SB4-208
ComponentsCarbonic anhydrase IX-mimic
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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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-Q71 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.306 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 IX-mimic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1263
Polymers28,8441
Non-polymers2822
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.193, 41.587, 72.094
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 IX-mimic


Mass: 28844.465 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 / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 42.24 %
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: 1.306→32.18 Å / Num. obs: 57349 / % possible obs: 97.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.023 / Rrim(I) all: 0.042 / Net I/σ(I): 17.7
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
1.31-1.331.70.45370321230.6850.3940.6011.673.1
7.15-32.183.10.02412003830.9980.0150.02852.298

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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: 1.306→30.443 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.03
RfactorNum. reflection% reflection
Rfree0.1732 2802 4.89 %
Rwork0.1611 --
obs0.1617 57316 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.34 Å2 / Biso mean: 22.07 Å2 / Biso min: 8.24 Å2
Refinement stepCycle: final / Resolution: 1.306→30.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 19 187 2248
Biso mean--13.69 26.84 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082136
X-RAY DIFFRACTIONf_angle_d1.0842907
X-RAY DIFFRACTIONf_chiral_restr0.085302
X-RAY DIFFRACTIONf_plane_restr0.01377
X-RAY DIFFRACTIONf_dihedral_angle_d15.99777
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3061-1.32860.28971210.2843202273
1.3286-1.35270.27161440.2581239987
1.3527-1.37880.24751390.2234258093
1.3788-1.40690.20751520.205273598
1.4069-1.43750.20691330.1955277299
1.4375-1.47090.21391370.1787276999
1.4709-1.50770.2071270.1792276599
1.5077-1.54850.18031280.176279699
1.5485-1.5940.18491580.1607274599
1.594-1.64550.17261550.16052791100
1.6455-1.70430.18171350.15712780100
1.7043-1.77250.15531030.1589283999
1.7725-1.85320.16561390.15732800100
1.8532-1.95090.18431460.1534275399
1.9509-2.07310.15991670.1536278999
2.0731-2.23310.15051650.1512774100
2.2331-2.45770.17441060.1515286699
2.4577-2.81320.17711470.1612821100
2.8132-3.54340.18931430.1651283599
3.5434-30.4430.13961570.1429288399
Refinement TLS params.Method: refined / Origin x: -30.4508 Å / Origin y: -1.4661 Å / Origin z: 16.2811 Å
111213212223313233
T0.0976 Å2-0.0036 Å20.0019 Å2-0.0953 Å20.0048 Å2--0.0984 Å2
L0.7557 °20.0509 °20.0116 °2-0.6566 °2-0.1156 °2--0.6799 °2
S-0.0218 Å °0.0151 Å °0.0436 Å °-0.0375 Å °0.038 Å °-0.0117 Å °0.0279 Å °-0.0005 Å °0.0206 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 194
4X-RAY DIFFRACTION1allC1

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