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- PDB-6gxb: Carbonic Anhydrase CAIX mimic in complex with inhibitor JS13 -

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Basic information

Entry
Database: PDB / ID: 6gxb
TitleCarbonic Anhydrase CAIX mimic in complex with inhibitor JS13
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic Anhydrase / CAII mutant to CAIX mimic / CA Inhibitor
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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-FF5 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBrynda, J. / Rezacova, P. / Pospisilova, K.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGA15-05677S Czech Republic
CitationJournal: Acs Omega / Year: 2019
Title: Inhibitor-Polymer Conjugates as a Versatile Tool for Detection and Visualization of Cancer-Associated Carbonic Anhydrase Isoforms
Authors: Pospisilova, K. / Knedlik, T. / Brynda, J. / Rezacova, P. / Sacha, P. / Schimer, J. / Kral, V. / Cigler, P. / Navratil, V. / Subr, V. / Konvalinka, J.
History
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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)29,3303
Polymers28,8441
Non-polymers4862
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.820, 41.150, 72.010
Angle α, β, γ (deg.)90.00, 103.81, 90.00
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-FF5 / ~{N}-[4-[4-[(4-sulfamoylphenyl)carbamoylamino]phenoxy]butyl]ethanamide


Mass: 420.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N4O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: protein 25 mg/mL, 1.6M sodium citrate, 50mM Tris H2SO4 pH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 22, 2017
RadiationMonochromator: VariMax ARC)SEC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.35→40.61 Å / Num. obs: 41518 / % possible obs: 79.1 % / Redundancy: 3.704 % / Biso Wilson estimate: 17.073 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.035 / Χ2: 1.022 / Net I/σ(I): 28.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.392.8590.2993.3620620.8720.36553.8
1.39-1.422.9320.2594.0222190.9110.31458.9
1.42-1.462.9190.2174.8423080.9320.26362.9
1.46-1.512.9250.1786.0123790.9540.21667
1.51-1.562.930.1556.9324400.9640.18971
1.56-1.612.8990.1268.4524360.9770.15372.9
1.61-1.672.7940.1129.625140.9810.13777.6
1.67-1.742.7810.09211.6425070.9880.11381.1
1.74-1.822.7670.07414.7224910.9920.0983.7
1.82-1.913.0260.06220.0224440.9930.07486
1.91-2.013.440.04726.3223760.9970.05587.2
2.01-2.134.4650.04235.3823790.9980.04893.1
2.13-2.284.6970.03542.5822780.9990.03994.1
2.28-2.465.5550.03350.821370.9990.03694.6
2.46-2.75.5640.02954.3720120.9990.03297
2.7-3.025.4170.02463.74181610.02696.2
3.02-3.495.1860.01975.2163310.02197.2
3.49-4.274.9450.01583.24138410.01798.2
4.27-6.044.2360.01678.08108510.01997.5
6.04-40.614.6420.01683.8261810.01897.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PO6

3po6


Resolution: 1.35→40.61 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.472 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15376 1038 2.5 %RANDOM
Rwork0.11277 ---
obs0.11381 40480 79.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0.16 Å2
2--0.11 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.35→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 30 287 2347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0142220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171964
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.6683043
X-RAY DIFFRACTIONr_angle_other_deg1.2441.6614634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5724110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50715365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.334157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022513
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02429
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4241.1011066
X-RAY DIFFRACTIONr_mcbond_other1.3251.0991065
X-RAY DIFFRACTIONr_mcangle_it1.71.6581340
X-RAY DIFFRACTIONr_mcangle_other1.7081.661341
X-RAY DIFFRACTIONr_scbond_it1.991.331154
X-RAY DIFFRACTIONr_scbond_other1.9891.3291155
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3561.9011689
X-RAY DIFFRACTIONr_long_range_B_refined2.67914.5422611
X-RAY DIFFRACTIONr_long_range_B_other2.50213.9462539
X-RAY DIFFRACTIONr_rigid_bond_restr2.86734184
X-RAY DIFFRACTIONr_sphericity_free16.8895164
X-RAY DIFFRACTIONr_sphericity_bonded6.96354233
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 51 -
Rwork0.165 2009 -
obs--53.81 %

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