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- PDB-6oud: Carbonic Anhydrase IX mimic complexed with benzene sulfonamide MB... -

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Basic information

Entry
Database: PDB / ID: 6oud
TitleCarbonic Anhydrase IX mimic complexed with benzene sulfonamide MB11-694B
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / benzene sulfonamide / carbonic anhydrase / 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-N7M / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.256 Å
AuthorsKota, A. / McKenna, R.
CitationJournal: To Be Published
Title: Carbonic Anhydrase IX mimic complexed with benzene sulfonamide MB11-694B
Authors: Kota, A. / McKenna, R.
History
DepositionMay 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5996
Polymers28,8441
Non-polymers7545
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.885, 40.965, 71.511
Angle α, β, γ (deg.)90.000, 103.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A
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

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Non-polymers , 5 types, 281 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-N7M / 4-{[(2-hydroxyethyl)carbamoyl]amino}benzene-1-sulfonamide


Mass: 259.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M sodium citrate, 50mM Tris Hal, pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.256→31.95 Å / Num. obs: 60937 / % possible obs: 95 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.51 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.02
Reflection shellResolution: 1.256→1.301 Å / Rmerge(I) obs: 0.88 / Num. unique obs: 5768

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10pre_2097refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.256→31.948 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.57
RfactorNum. reflection% reflection
Rfree0.1905 3004 4.93 %
Rwork0.1737 --
obs0.1746 60925 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.85 Å2 / Biso mean: 21.149 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.256→31.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 45 280 2367
Biso mean--30.95 31.54 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092183
X-RAY DIFFRACTIONf_angle_d1.2162971
X-RAY DIFFRACTIONf_chiral_restr0.094306
X-RAY DIFFRACTIONf_plane_restr0.009387
X-RAY DIFFRACTIONf_dihedral_angle_d14.095797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2563-1.27690.42021350.36522545268086
1.2769-1.29890.33251410.32282648278993
1.2989-1.32250.33681430.30232649279292
1.3225-1.34790.29271510.27482652280392
1.3479-1.37550.24271450.24812723286894
1.3755-1.40540.24321150.23492743285893
1.4054-1.43810.24561450.21722702284794
1.4381-1.4740.24271510.21332745289695
1.474-1.51390.23621490.20162716286594
1.5139-1.55840.22251540.19482741289594
1.5584-1.60870.21811380.18382763290195
1.6087-1.66620.18281260.17962778290495
1.6662-1.73290.18351480.17672760290895
1.7329-1.81180.1991190.17692797291696
1.8118-1.90730.1631640.17312801296596
1.9073-2.02680.15511230.16432831295497
2.0268-2.18320.20061360.16272841297796
2.1832-2.40290.17061550.15842843299897
2.4029-2.75040.19211400.17432871301197
2.7504-3.46460.18311750.15732837301297
3.4646-31.95780.15471510.13992935308697

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