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- PDB-6u4t: Carbonic anhydrase 9 in complex with SB4197 -

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Basic information

Entry
Database: PDB / ID: 6u4t
TitleCarbonic anhydrase 9 in complex with SB4197
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Inhibitor / Complex / cyclical sulfonamide / 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 / morphogenesis of an epithelium ...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 / 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 / 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-PX7 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.356 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
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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)29,3344
Polymers28,8441
Non-polymers4903
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.153, 41.470, 72.050
Angle α, β, γ (deg.)90.000, 103.840, 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
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PX7 / 4-methyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione


Mass: 212.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 41.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6 M NaCitrate, 50 mM Tris

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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: Aug 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.356→32.14 Å / Num. obs: 52421 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 25.9
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
1.36-1.384.50.5561090124030.780.2870.632.492.6
7.43-32.146.20.021219735210.0090.02380.298.7

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Processing

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

3ks3


Resolution: 1.356→30.428 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.17
RfactorNum. reflection% reflection
Rfree0.1729 2577 4.92 %
Rwork0.154 --
obs0.1549 52400 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.67 Å2 / Biso mean: 21.9586 Å2 / Biso min: 8.5 Å2
Refinement stepCycle: final / Resolution: 1.356→30.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 37 193 2272
Biso mean--25.83 27.35 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082171
X-RAY DIFFRACTIONf_angle_d1.1192961
X-RAY DIFFRACTIONf_chiral_restr0.182306
X-RAY DIFFRACTIONf_plane_restr0.009384
X-RAY DIFFRACTIONf_dihedral_angle_d14.434787
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.356-1.38170.26571400.2345255693
1.3817-1.40990.21381180.19852791100
1.4099-1.44060.21011470.181274199
1.4406-1.47410.2021610.17192728100
1.4741-1.5110.17141650.16532756100
1.511-1.55180.18691430.16212754100
1.5518-1.59750.19471610.15012760100
1.5975-1.6490.16671430.15252736100
1.649-1.7080.18281370.15072773100
1.708-1.77640.18631430.15222773100
1.7764-1.85720.16581280.15232799100
1.8572-1.95510.18241360.14552782100
1.9551-2.07760.17511640.14672753100
2.0776-2.23790.16571220.14532834100
2.2379-2.4630.16611300.14852798100
2.463-2.81920.15361500.16012787100
2.8192-3.55110.18891440.16282814100
3.5511-30.4280.15151450.14122888100
Refinement TLS params.Method: refined / Origin x: -30.3843 Å / Origin y: -1.3746 Å / Origin z: 16.1824 Å
111213212223313233
T0.1028 Å2-0.0024 Å20.0027 Å2-0.1003 Å20.002 Å2--0.1045 Å2
L0.7516 °20.0486 °20.0567 °2-0.6893 °2-0.0946 °2--0.7184 °2
S-0.0267 Å °0.0115 Å °0.0417 Å °-0.035 Å °0.0339 Å °-0.0051 Å °0.0191 Å °-0.002 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 - 198
4X-RAY DIFFRACTION1allC1 - 2

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