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- PDB-6u4q: Carbonic anhydrase 2 in complex with SB4197 -

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Basic information

Entry
Database: PDB / ID: 6u4q
TitleCarbonic anhydrase 2 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 / 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-PX7 / 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
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)29,2103
Polymers28,9331
Non-polymers2782
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.342, 41.226, 72.096
Angle α, β, γ (deg.)90.000, 104.250, 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: 28932.641 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.: 1 / Source method: obtained synthetically / Formula: C8H8N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 41.65 %
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: BL9-2 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.306→34.94 Å / Num. obs: 54433 / % possible obs: 92.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 21.2
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
1.31-1.334.50.589736316390.7760.3010.6662.356.5
7.15-34.946.10.03223843880.9990.0130.03454.798.8

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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: 1.306→29.085 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.48
RfactorNum. reflection% reflection
Rfree0.1665 2676 4.92 %
Rwork0.1512 --
obs0.152 54415 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.44 Å2 / Biso mean: 18.4899 Å2 / Biso min: 6.79 Å2
Refinement stepCycle: final / Resolution: 1.306→29.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 21 203 2273
Biso mean--19.46 24.41 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082138
X-RAY DIFFRACTIONf_angle_d1.0932907
X-RAY DIFFRACTIONf_chiral_restr0.082301
X-RAY DIFFRACTIONf_plane_restr0.009377
X-RAY DIFFRACTIONf_dihedral_angle_d14.557780
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.31-1.32960.184900.2378166857
1.3296-1.35520.20071100.2072195169
1.3552-1.38290.23221260.1932247383
1.3829-1.4130.20461300.1898275994
1.413-1.44580.20031040.1871279795
1.4458-1.4820.21461230.1695283896
1.482-1.5220.18761440.1562280095
1.522-1.56680.18451630.1504277995
1.5668-1.61740.15091570.15277396
1.6174-1.67520.18161350.1482284697
1.6752-1.74230.14911600.1445284297
1.7423-1.82150.16341540.1464281097
1.8215-1.91760.15471540.1476285697
1.9176-2.03770.17031500.1409287298
2.0377-2.1950.14781710.1372288798
2.195-2.41570.15621270.1404290298
2.4157-2.76510.16291600.1542292499
2.7651-3.48280.19121450.1588295599
3.4828-29.0850.1481730.1418300799
Refinement TLS params.Method: refined / Origin x: 11.5466 Å / Origin y: -1.7409 Å / Origin z: 16.0044 Å
111213212223313233
T0.0781 Å2-0.0032 Å20.001 Å2-0.074 Å20.0016 Å2--0.0798 Å2
L0.5749 °2-0.0636 °20.044 °2-0.3702 °20.0257 °2--0.5742 °2
S-0.0071 Å °-0.0135 Å °0.0122 Å °-0.0204 Å °0.0035 Å °-0.0011 Å °0.0145 Å °-0.002 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 209
4X-RAY DIFFRACTION1allC1

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