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- PDB-4zwz: Engineered Carbonic Anhydrase IX mimic in complex with a glucosyl... -

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Basic information

Entry
Database: PDB / ID: 4zwz
TitleEngineered Carbonic Anhydrase IX mimic in complex with a glucosyl sulfamate inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Carbonic Anhydrase IX mimic / 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 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 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
methyl / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsMahon, B.P. / Lomelino, C.L. / Driscoll, J.M. / McKenna, R.
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 1.2Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 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)29,5175
Polymers28,8441
Non-polymers6724
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint6 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.695, 41.096, 71.430
Angle α, β, γ (deg.)90.000, 103.740, 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 / Fragment: UNP residues 4-260 / 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: Sugar ChemComp-510 / methyl (2S,4R)-1-[(2S,3R,4R,5S,6S)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfonyl-4-sulfamoyloxy-pyrrolidine-2-carbox ylate


Type: L-saccharide / Mass: 450.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O12S2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
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 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→20 Å / Num. obs: 27416 / % possible obs: 90.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.83 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.025 / Rrim(I) all: 0.05 / Χ2: 0.785 / Net I/av σ(I): 24.343 / Net I/σ(I): 13 / Num. measured all: 96724
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.653.50.64415120.7460.3730.7480.47299.9
1.65-1.683.50.55615160.7640.3170.6430.50399.9
1.68-1.713.60.45714810.8220.2590.5280.53299.9
1.71-1.753.50.38215240.8760.2160.4410.52599.4
1.75-1.783.50.34714800.8840.1970.4010.65997.8
1.78-1.823.50.26214650.9160.150.3030.68797.5
1.82-1.873.50.20914320.9470.1190.2420.61396
1.87-1.923.60.16514390.9610.0950.1910.64694.2
1.92-1.983.60.13913560.970.0810.1620.69489.9
1.98-2.043.70.11513460.9790.0660.1340.66889.1
2.04-2.113.70.08912950.9870.0510.1030.984.9
2.11-2.23.60.06812460.990.0390.0790.83382.8
2.2-2.33.70.05912100.9930.0330.0680.85679.8
2.3-2.423.60.04511930.9950.0260.0520.7678.3
2.42-2.573.50.04311670.9960.0240.0490.70276.7
2.57-2.773.30.05112060.9940.0290.0592.32178.9
2.77-3.053.10.03512660.9940.0210.0411.01283.1
3.05-3.483.20.03414190.9940.0220.0411.03191.8
3.48-4.383.40.0313470.9960.0190.0360.96987.6
4.38-203.80.02515160.9980.0150.0290.82595.1

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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: 1.62→19.749 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 1300 5.04 %random selection
Rwork0.1607 35085 --
obs0.1633 27416 61.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.35 Å2 / Biso mean: 21.6383 Å2 / Biso min: 8.81 Å2
Refinement stepCycle: final / Resolution: 1.62→19.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 37 232 2311
Biso mean--47.07 30.06 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062180
X-RAY DIFFRACTIONf_angle_d1.192972
X-RAY DIFFRACTIONf_chiral_restr0.049322
X-RAY DIFFRACTIONf_plane_restr0.006377
X-RAY DIFFRACTIONf_dihedral_angle_d14.314792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.65310.2685940.23651808190241
1.6531-1.70170.31081110.21852165227650
1.7017-1.75660.28591170.22212203232050
1.7566-1.81930.22571160.21122169228550
1.8193-1.89210.21321140.18552168228250
1.8921-1.97820.21221130.17022224233751
1.9782-2.08240.19811340.16252589272359
2.0824-2.21270.20181750.15163083325871
2.2127-2.38320.21841650.16033123328872
2.3832-2.62260.25281580.17033069322770
2.6226-3.00090.23421670.17293059322670
3.0009-3.77650.23081980.14853530372881
3.7765-19.75010.15392020.1363895409789
Refinement TLS params.Method: refined / Origin x: 11.8569 Å / Origin y: -1.4328 Å / Origin z: 15.8297 Å
111213212223313233
T0.1072 Å20.0009 Å20.0044 Å2-0.1045 Å20.002 Å2--0.103 Å2
L0.6524 °2-0.114 °20.1773 °2-0.4703 °2-0.1142 °2--0.3472 °2
S-0.0191 Å °-0.0003 Å °0.0281 Å °-0.0209 Å °0.0239 Å °0.005 Å °-0.0163 Å °0.0307 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 118
4X-RAY DIFFRACTION1allD120 - 240
5X-RAY DIFFRACTION1allC1
6X-RAY DIFFRACTION1allE2
7X-RAY DIFFRACTION1allE3

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