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- PDB-6ugq: Human Carbonic Anhydrase IX-mimic complexed with SB4-206 -

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Basic information

Entry
Database: PDB / ID: 6ugq
TitleHuman Carbonic Anhydrase IX-mimic complexed with SB4-206
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 / 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-Q7A / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.305 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)29,3754
Polymers28,8441
Non-polymers5313
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.128, 41.450, 72.030
Angle α, β, γ (deg.)90.000, 103.950, 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-Q7A / 5-chloro-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione


Mass: 232.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
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: 1.305→34.95 Å / Num. obs: 54512 / % possible obs: 92.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.018 / Rrim(I) all: 0.034 / 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
1.31-1.332.30.292393717100.8760.2120.3632.957.2
7.03-34.953.10.01812614050.9990.0110.02166.798.1

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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: 1.305→30.438 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.25
RfactorNum. reflection% reflection
Rfree0.163 2632 4.83 %
Rwork0.1526 --
obs0.1531 54492 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.49 Å2 / Biso mean: 19.7319 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 1.305→30.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 37 200 2279
Biso mean--17.92 25.18 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092148
X-RAY DIFFRACTIONf_angle_d1.1412927
X-RAY DIFFRACTIONf_chiral_restr0.189302
X-RAY DIFFRACTIONf_plane_restr0.01378
X-RAY DIFFRACTIONf_dihedral_angle_d15.61779
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3053-1.32910.2471940.2319165857
1.3291-1.35460.22761080.2103198968
1.3546-1.38230.22791350.1927246785
1.3823-1.41240.2151480.1715269492
1.4124-1.44520.19991270.1713280295
1.4452-1.48130.20091410.1639281696
1.4813-1.52140.17481220.1597280996
1.5214-1.56620.16541460.1533279995
1.5662-1.61670.16031510.1474280196
1.6167-1.67450.16321630.1451282397
1.6745-1.74150.13771150.1435289797
1.7415-1.82080.13481180.1477287597
1.8208-1.91680.15461520.1472287197
1.9168-2.03680.16451680.1427286198
2.0368-2.19410.15781630.148289998
2.1941-2.41480.1511190.1454290698
2.4148-2.7640.17941500.1544294699
2.764-3.48150.16311510.1591294399
3.4815-30.4380.14531610.1456300499
Refinement TLS params.Method: refined / Origin x: -30.4131 Å / Origin y: -1.5997 Å / Origin z: 16.1559 Å
111213212223313233
T0.0851 Å2-0.0011 Å20.0014 Å2-0.0848 Å20.004 Å2--0.0881 Å2
L0.6522 °2-0.0245 °20.015 °2-0.6453 °2-0.1243 °2--0.6288 °2
S-0.0094 Å °-0.0018 Å °0.0331 Å °-0.0348 Å °0.024 Å °-0.0055 Å °0.0206 Å °-0.0026 Å °0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 204
4X-RAY DIFFRACTION1allC1 - 2

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