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- PDB-6e92: CA IX mimic Complexed with Steroidal Sulfamate Compound STX 2845 -

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Basic information

Entry
Database: PDB / ID: 6.0E+92
TitleCA IX mimic Complexed with Steroidal Sulfamate Compound STX 2845
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic Anhydrase Steroid Sulfamate Cancer
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 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-HZY / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.772 Å
AuthorsAndring, J.T. / Mckenna, R.
CitationJournal: J. Med. Chem. / Year: 2019
Title: 3,17 beta-Bis-sulfamoyloxy-2-methoxyestra-1,3,5(10)-triene and Nonsteroidal Sulfamate Derivatives Inhibit Carbonic Anhydrase IX: Structure-Activity Optimization for Isoform Selectivity.
Authors: Andring, J.T. / Dohle, W. / Tu, C. / Potter, B.V.L. / McKenna, R.
History
DepositionJul 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: 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)29,3153
Polymers28,8441
Non-polymers4712
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.487, 41.733, 72.611
Angle α, β, γ (deg.)90.000, 104.030, 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-HZY / 6-(sulfamoyloxy)-2-[(3,4,5-trimethoxyphenyl)methyl]isoquinolin-2-ium


Mass: 405.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N2O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M NaCitrate 50mM Tris

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 31356 / % possible obs: 93.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.86 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Χ2: 0.869 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.83.40.3649420.8630.2260.4290.87979.2
1.8-1.833.60.30411020.880.1880.3590.8790.5
1.83-1.873.60.24311250.9180.150.2860.84991.5
1.87-1.913.60.20511130.9530.1270.2420.88692.7
1.91-1.953.60.17610980.960.1090.2070.87191.3
1.95-1.993.60.14711350.9680.0910.1730.9393.2
1.99-2.043.60.12811250.9740.0780.150.95893
2.04-2.13.60.11211190.9810.0690.1310.92893.2
2.1-2.163.50.09511340.9850.0590.1121.01294
2.16-2.233.60.08311290.9880.0510.0980.93793.2
2.23-2.313.60.07311780.9920.0450.0860.89695.5
2.31-2.43.60.06511420.9920.040.0770.84894.9
2.4-2.513.60.0611530.9940.0370.0710.90394.5
2.51-2.643.60.05411660.9950.0340.0640.87796
2.64-2.813.60.04711800.9960.0290.0550.87496.3
2.81-3.033.50.0411840.9960.0250.0480.81496.4
3.03-3.333.60.03311780.9970.0210.0390.78397.4
3.33-3.813.50.03112210.9960.0190.0370.77798.1
3.81-4.83.50.02912120.9970.0180.0340.74698
4.8-503.40.02912660.9970.0170.0340.76798.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10pre_2097refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.772→29.327 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.53
RfactorNum. reflection% reflection
Rfree0.1891 1580 5.04 %
Rwork0.1514 --
obs0.1532 31356 66.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.95 Å2 / Biso mean: 23.2475 Å2 / Biso min: 7.68 Å2
Refinement stepCycle: final / Resolution: 1.772→29.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 29 55 2126
Biso mean--48.36 28.23 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082188
X-RAY DIFFRACTIONf_angle_d1.4212983
X-RAY DIFFRACTIONf_chiral_restr0.07307
X-RAY DIFFRACTIONf_plane_restr0.012387
X-RAY DIFFRACTIONf_dihedral_angle_d10.3842209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7725-1.82970.2563930.20771868196146
1.8297-1.89510.23061040.17521909201347
1.8951-1.97090.2078920.17541927201947
1.9709-2.06060.20111020.17351923202548
2.0606-2.16920.22481090.16491996210549
2.1692-2.30510.20721160.1662288240455
2.3051-2.4830.17671530.16832789294269
2.483-2.73270.2091880.17793398358684
2.7327-3.12770.21852040.18023835403994
3.1277-3.93910.19972060.13633905411196
3.9391-29.33080.13792130.11433938415197
Refinement TLS params.Method: refined / Origin x: -9.3933 Å / Origin y: -1.7013 Å / Origin z: 16.1267 Å
111213212223313233
T0.0949 Å2-0.0008 Å20.0024 Å2-0.0898 Å20.0013 Å2--0.0975 Å2
L0.7036 °2-0.026 °20.0705 °2-0.4451 °2-0.1165 °2--0.6593 °2
S-0.0123 Å °-0.0081 Å °0.0327 Å °-0.0181 Å °0.0224 Å °-0.0162 Å °0.0059 Å °0.0107 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 - 38
4X-RAY DIFFRACTION1allD39 - 56
5X-RAY DIFFRACTION1allC1

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