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- PDB-7jnx: Carbonic Anhydrase II Complexed with N-(5-sulfamoyl-1,3,4-thiadia... -

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Basic information

Entry
Database: PDB / ID: 7jnx
TitleCarbonic Anhydrase II Complexed with N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)pivalamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/INHIBITOR / Carbonic Anhydrase / CA Inhibitor / Structure Guided Drug Design / Carbonic Anhydrase II / Carbonic Anhydrase IX / CAII / CAIX / Sulfonamide / 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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
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-VGS / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.286 Å
AuthorsAndring, J.T. / McKenna, R.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis of Nanomolar Inhibition of Tumor-Associated Carbonic Anhydrase IX: X-Ray Crystallographic and Inhibition Study of Lipophilic Inhibitors with Acetazolamide Backbone.
Authors: Andring, J.T. / Fouch, M. / Akocak, S. / Angeli, A. / Supuran, C.T. / Ilies, M.A. / McKenna, R.
History
DepositionAug 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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)29,7895
Polymers29,2891
Non-polymers5004
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.017, 41.028, 71.476
Angle α, β, γ (deg.)90.000, 104.450, 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: 29289.062 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

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Non-polymers , 5 types, 224 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-VGS / 2,2-dimethyl-N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)propanamide


Mass: 264.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12N4O3S2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M Sodium Citrate, 50mM Tris

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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: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.286→31.78 Å / Num. obs: 57496 / % possible obs: 95.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 9.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.031 / Rrim(I) all: 0.07 / Net I/σ(I): 14
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
1.29-1.311.50.38245216810.7560.3220.5011.757
7.05-31.784.60.03618063930.9980.0180.0435.898.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.286→25.125 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1762 2868 4.99 %
Rwork0.1589 54606 -
obs0.1598 57474 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.71 Å2 / Biso mean: 13.7922 Å2 / Biso min: 5.1 Å2
Refinement stepCycle: final / Resolution: 1.286→25.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 33 220 2302
Biso mean--14.41 22.41 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072221
X-RAY DIFFRACTIONf_angle_d1.1043026
X-RAY DIFFRACTIONf_chiral_restr0.081309
X-RAY DIFFRACTIONf_plane_restr0.006398
X-RAY DIFFRACTIONf_dihedral_angle_d15.031821
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2863-1.30840.3174610.2724163657
1.3084-1.33220.28811050.2365215576
1.3322-1.35790.26321030.2131246286
1.3579-1.38560.23271310.187269296
1.3856-1.41570.18641610.17582851100
1.4157-1.44860.20061420.17142846100
1.4486-1.48480.20321510.15912801100
1.4848-1.5250.19111540.15782853100
1.525-1.56990.17081760.15362813100
1.5699-1.62050.171520.15032862100
1.6205-1.67840.16691560.15592844100
1.6784-1.74560.20271560.15022820100
1.7456-1.8250.16681580.15772838100
1.825-1.92120.15551300.15612865100
1.9212-2.04150.18881660.15062863100
2.0415-2.19910.15951370.14742847100
2.1991-2.42020.16751480.15412866100
2.4202-2.77010.17241670.16472852100
2.7701-3.48850.17521770.16032871100
3.4885-25.1250.14821370.14342969100
Refinement TLS params.Method: refined / Origin x: -9.3932 Å / Origin y: -1.4103 Å / Origin z: 15.9488 Å
111213212223313233
T0.0549 Å2-0.0009 Å2-0 Å2-0.0531 Å20.0001 Å2--0.0601 Å2
L0.5018 °2-0.0673 °2-0.0109 °2-0.3693 °2-0.0222 °2--0.5975 °2
S-0.0004 Å °-0.0179 Å °0.0176 Å °-0.0187 Å °0.0042 Å °0.0034 Å °0.0167 Å °0.0005 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB400
3X-RAY DIFFRACTION1allC262
4X-RAY DIFFRACTION1allE1 - 154
5X-RAY DIFFRACTION1allE155 - 223
6X-RAY DIFFRACTION1allD1
7X-RAY DIFFRACTION1allF1

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