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- PDB-6otm: Carbonic Anhydrase IX mimic complexed with ureic benzene sulfonam... -

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Basic information

Entry
Database: PDB / ID: 6otm
TitleCarbonic Anhydrase IX mimic complexed with ureic benzene sulfonamide MB10-586B
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / ureido 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 / 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, 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-N8A / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.307 Å
AuthorsKota, A. / McKenna, R.
CitationJournal: To Be Published
Title: Carbonic Anhydrase IX mimic complexed with ureido benzene sulfonamide MB9-561B
Authors: Kota, A. / McKenna, R.
History
DepositionMay 3, 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)29,4305
Polymers28,8441
Non-polymers5864
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.879, 41.193, 71.976
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 / 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-N8A / 4-hydroxy-3-({[2-(pyridin-2-yl)ethyl]carbamoyl}amino)benzene-1-sulfonamide


Mass: 336.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 41.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M Sodium Citrate, 50mM Tris-HCl, 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: 1.307→31.98 Å / Num. obs: 57560 / % possible obs: 100 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.46 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.75
Reflection shellResolution: 1.307→1.354 Å / Rmerge(I) obs: 0.56 / Num. unique obs: 5594

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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: 1.307→31.978 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.59
RfactorNum. reflection% reflection
Rfree0.1792 2771 4.81 %
Rwork0.1642 --
obs0.1649 57557 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.28 Å2 / Biso mean: 18.226 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: final / Resolution: 1.307→31.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 36 324 2402
Biso mean--27.77 29.76 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112160
X-RAY DIFFRACTIONf_angle_d1.2022936
X-RAY DIFFRACTIONf_chiral_restr0.094305
X-RAY DIFFRACTIONf_plane_restr0.009380
X-RAY DIFFRACTIONf_dihedral_angle_d13.729792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3075-1.330.31761340.30672590272496
1.33-1.35420.26431410.26842729287099
1.3542-1.38020.26051330.239827322865100
1.3802-1.40840.25111140.219327392853100
1.4084-1.4390.22341380.200527572895100
1.439-1.47250.2421490.199427152864100
1.4725-1.50930.20951510.181827092860100
1.5093-1.55010.17711420.18627362878100
1.5501-1.59580.18251310.174327432874100
1.5958-1.64730.21051290.16727362865100
1.6473-1.70610.18321340.168627232857100
1.7061-1.77440.18371500.162127412891100
1.7744-1.85520.19451620.159227152877100
1.8552-1.9530.18831340.157627622896100
1.953-2.07530.17051480.155927332881100
2.0753-2.23550.16711580.152627342892100
2.2355-2.46040.15161470.156927662913100
2.4604-2.81630.16361420.159927472889100
2.8163-3.54750.17051090.150628062915100
3.5475-31.98730.14931250.143428732998100

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