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- PDB-4zwy: Human Carbonic Anhydrase II in complex with a glucosyl sulfamate ... -

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Basic information

Entry
Database: PDB / ID: 4zwy
TitleHuman Carbonic Anhydrase II in complex with a glucosyl sulfamate inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLyase/Lyase inhibitor / Carbonic anhydrase II / glucosyl sulfamate / inhibitor complex. / 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 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-4SN / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMahon, B.P. / Lomelino, C.L. / Driscoll, J.M. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA165284 United States
CitationJournal: J.Med.Chem. / Year: 2015
Title: Mapping Selective Inhibition of the Cancer-Related Carbonic Anhydrase IX Using Structure-Activity Relationships of Glucosyl-Based Sulfamates.
Authors: Mahon, B.P. / Lomelino, C.L. / Ladwig, J. / Rankin, G.M. / Driscoll, J.M. / Salguero, A.L. / Pinard, M.A. / Vullo, D. / Supuran, C.T. / Poulsen, S.A. / McKenna, R.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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)29,6674
Polymers28,9331
Non-polymers7343
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.178, 41.344, 71.816
Angle α, β, γ (deg.)90.000, 104.120, 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: 28932.641 Da / Num. of mol.: 1 / Fragment: UNP residues 4-260
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-4SN / (6S)-1,3,4,5-tetra-O-acetyl-2,6-anhydro-6-{[5-(sulfamoyloxy)pentyl]sulfamoyl}-L-altritol


Mass: 576.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H32N2O14S2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-HCl pH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 38042 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.17 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Χ2: 2.576 / Net I/av σ(I): 47.194 / Net I/σ(I): 32 / Num. measured all: 126969
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5330.32118850.9080.2160.3891.91498.1
1.53-1.553.20.28518700.9280.1850.3411.91797.4
1.55-1.583.20.24318720.9340.1560.292.03697.7
1.58-1.623.20.19618420.9590.1240.2332.05896
1.62-1.653.20.16518790.9670.1050.1962.21996.1
1.65-1.693.30.13718410.9750.0880.1642.22495.5
1.69-1.733.30.1118350.9840.070.1312.23395.8
1.73-1.783.30.09318300.9890.0590.1112.21696.3
1.78-1.833.30.07618820.9910.0480.0912.14596.8
1.83-1.893.30.06419100.9920.0410.0772.16898.2
1.89-1.963.30.05319100.9940.0340.0642.199
1.96-2.043.30.04819010.9960.0310.0582.22199.4
2.04-2.133.30.04319300.9960.0280.0512.13499.4
2.13-2.243.40.04119430.9960.0260.0492.25299.5
2.24-2.383.40.03819180.9960.0250.0462.32599.5
2.38-2.563.50.03919630.9960.0250.0462.46799.8
2.56-2.823.60.03919360.9960.0240.0462.65999.9
2.82-3.233.60.04319450.9940.0270.0513.40199.7
3.23-4.073.60.04719490.9930.030.0554.61399.4
4.07-503.50.04520010.9950.0280.0535.13398.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.5→32.024 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 1902 5 %random selection
Rwork0.1553 36123 --
obs0.1563 38025 97.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.08 Å2 / Biso mean: 24.1905 Å2 / Biso min: 12.65 Å2
Refinement stepCycle: final / Resolution: 1.5→32.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 38 285 2372
Biso mean--41.19 34.69 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062187
X-RAY DIFFRACTIONf_angle_d1.3242974
X-RAY DIFFRACTIONf_chiral_restr0.048313
X-RAY DIFFRACTIONf_plane_restr0.006382
X-RAY DIFFRACTIONf_dihedral_angle_d13.435802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53550.27221170.22622481X-RAY DIFFRACTION95
1.5355-1.5770.23471410.20462523X-RAY DIFFRACTION97
1.577-1.62340.26051360.21282551X-RAY DIFFRACTION96
1.6234-1.67580.19891320.1872504X-RAY DIFFRACTION96
1.6758-1.73570.18481420.15742496X-RAY DIFFRACTION95
1.7357-1.80520.21041230.15762536X-RAY DIFFRACTION96
1.8052-1.88740.19331450.15312566X-RAY DIFFRACTION98
1.8874-1.98690.18041300.15262592X-RAY DIFFRACTION99
1.9869-2.11130.18461350.14612650X-RAY DIFFRACTION99
2.1113-2.27430.17171390.15172591X-RAY DIFFRACTION99
2.2743-2.50310.1561380.152638X-RAY DIFFRACTION100
2.5031-2.86510.17151400.16132637X-RAY DIFFRACTION100
2.8651-3.6090.16611430.14932662X-RAY DIFFRACTION100
3.609-40.15561410.1462696X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -9.3397 Å / Origin y: -1.7058 Å / Origin z: 15.9139 Å
111213212223313233
T0.1462 Å2-0.0057 Å2-0.0006 Å2-0.1432 Å20.0015 Å2--0.1478 Å2
L0.6717 °2-0.14 °2-0.0443 °2-0.6664 °20.002 °2--0.6997 °2
S-0.0126 Å °-0.0198 Å °0.0141 Å °-0.0642 Å °0.0115 Å °0.0052 Å °0.0013 Å °0.0079 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allC1 - 127
4X-RAY DIFFRACTION1allC130 - 182
5X-RAY DIFFRACTION1allC183 - 189
6X-RAY DIFFRACTION1allC192 - 282
7X-RAY DIFFRACTION1allD1
8X-RAY DIFFRACTION1allE400

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