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- PDB-6ugo: Human Carbonic Anhydrase IX-mimic complexed with SB4-205 -

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Basic information

Entry
Database: PDB / ID: 6ugo
TitleHuman Carbonic Anhydrase IX-mimic complexed with SB4-205
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 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
CITRIC ACID / Chem-Q77 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.457 Å
AuthorsMurray, A.B. / McKenna, R. / Lomelino, C.L.
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)29,7816
Polymers28,8441
Non-polymers9365
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.147, 41.362, 72.047
Angle α, β, γ (deg.)90.000, 103.970, 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-Q77 / 5,7-dimethyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione


Mass: 226.252 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H10N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 41.78 %
Crystal growTemperature: 298 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: 1.457→32.09 Å / Num. obs: 41707 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.067 / Rrim(I) all: 0.125 / Net I/σ(I): 7.7
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
1.46-1.483.21.798632619810.2171.1522.1420.794.6
7.98-32.092.90.0368362850.9970.0250.04426.797.3

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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: 1.457→30.452 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.72
RfactorNum. reflection% reflection
Rfree0.203 2101 5.04 %
Rwork0.1751 --
obs0.1765 41673 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.22 Å2 / Biso mean: 22.9664 Å2 / Biso min: 8.03 Å2
Refinement stepCycle: final / Resolution: 1.457→30.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 91 179 2312
Biso mean--24.1 27.12 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082134
X-RAY DIFFRACTIONf_angle_d1.0972905
X-RAY DIFFRACTIONf_chiral_restr0.079300
X-RAY DIFFRACTIONf_plane_restr0.008373
X-RAY DIFFRACTIONf_dihedral_angle_d16.281771
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.457-1.49050.35161260.3542253596
1.4905-1.52770.30351240.3148262898
1.5277-1.56910.33621510.2881258497
1.5691-1.61520.26851600.2572258198
1.6152-1.66740.29231700.2318262099
1.6674-1.72690.23791490.2143262399
1.7269-1.79610.23381630.2027262199
1.7961-1.87780.26281260.187263899
1.8778-1.97680.19851390.1641264199
1.9768-2.10060.19081340.1545264798
2.1006-2.26280.18491190.1548266799
2.2628-2.49040.17031340.1568267399
2.4904-2.85050.22311180.1576269999
2.8505-3.59040.19671420.1578268099
3.5904-30.4520.13931460.1452273598
Refinement TLS params.Method: refined / Origin x: -30.3883 Å / Origin y: -1.3655 Å / Origin z: 16.1575 Å
111213212223313233
T0.0931 Å2-0.0023 Å20.0024 Å2-0.0932 Å2-0.0007 Å2--0.0945 Å2
L0.5998 °2-0.0569 °20.0774 °2-0.6657 °2-0.0671 °2--0.5376 °2
S-0.02 Å °-0.0174 Å °0.0205 Å °-0.0296 Å °0.0278 Å °-0.009 Å °0.0076 Å °0.0145 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 161
4X-RAY DIFFRACTION1allD162 - 185
5X-RAY DIFFRACTION1allC1 - 2
6X-RAY DIFFRACTION1allC3
7X-RAY DIFFRACTION1allE1

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