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- PDB-4zx1: Engineered Carbonic Anhydrase IX mimic in complex with a glucosyl... -

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Basic information

Entry
Database: PDB / ID: 4zx1
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 / 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-5L3 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.501 Å
AuthorsMahon, B.P. / Lomelino, C.L. / Salguero, A.L. / 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. / Moeker, 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 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_prerelease_seq ...chem_comp / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)29,5145
Polymers28,8431
Non-polymers6704
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint5 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.910, 41.270, 71.909
Angle α, β, γ (deg.)90.000, 103.710, 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: 28843.480 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: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Sugar ChemComp-5L3 / (6R)-5-O-acetyl-2,6-anhydro-6-{[4-(sulfamoyloxy)piperidin-1-yl]sulfonyl}-L-glucitol


Type: D-saccharide / Mass: 448.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H24N2O11S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details5L3 represents deacetylated ligand of glycoconjugate sulfamate compound 626 observed in the crystal structure.

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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: 41.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-HCl

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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 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→19.863 Å / Num. obs: 37841 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.17 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.063 / Rrim(I) all: 0.121 / Χ2: 0.659 / Net I/av σ(I): 9.345 / Net I/σ(I): 4.8 / Num. measured all: 126897
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.531.70.71814500.5030.6130.9490.18776.8
1.53-1.552.20.68118080.560.5190.8620.20194.2
1.55-1.582.80.62918910.6570.4370.770.21199.3
1.58-1.623.20.54418880.7330.3540.6520.21999.3
1.62-1.653.30.46819070.7780.2960.5560.22399.7
1.65-1.693.30.39719050.8310.2490.470.23999.6
1.69-1.733.40.33119190.8770.2070.3920.24499.8
1.73-1.783.40.27519030.9050.1720.3260.2799.9
1.78-1.833.40.22719050.9330.1410.2680.30799.9
1.83-1.893.50.219300.9490.1230.2360.35299.9
1.89-1.963.50.16318950.9550.10.1920.417100
1.96-2.043.60.14519050.9690.0880.170.464100
2.04-2.133.60.12619150.9650.0770.1490.643100
2.13-2.243.60.11119450.9750.0670.130.673100
2.24-2.383.60.10519090.9710.0630.1230.767100
2.38-2.563.60.10219430.9820.0620.1190.9100
2.56-2.823.70.09319170.9830.0560.1090.934100
2.82-3.233.70.08119560.9750.0490.0951.203100
3.23-4.063.70.08619380.9760.0520.11.8399.9
4.06-203.60.07220120.9820.0450.0851.686100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXdev_1839refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 1.501→19.863 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 1671 5.01 %random selection
Rwork0.1566 31667 --
obs0.1585 33338 86.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.36 Å2 / Biso mean: 21.1787 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 1.501→19.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 37 264 2343
Biso mean--43.53 31.88 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072180
X-RAY DIFFRACTIONf_angle_d1.1642974
X-RAY DIFFRACTIONf_chiral_restr0.048321
X-RAY DIFFRACTIONf_plane_restr0.005379
X-RAY DIFFRACTIONf_dihedral_angle_d13.46794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5013-1.54540.4998190.413243145014
1.5454-1.59530.3104910.271575166653
1.5953-1.65230.23921330.22992507264084
1.6523-1.71840.29571410.21962818295993
1.7184-1.79650.21531560.18972983313998
1.7965-1.89120.19481610.164830173178100
1.8912-2.00960.20861580.15330123170100
2.0096-2.16460.1941530.151830413194100
2.1646-2.38210.1961710.147930243195100
2.3821-2.7260.1941590.156430523211100
2.726-3.43160.17961650.146430783243100
3.4316-19.86520.17081640.136231293293100
Refinement TLS params.Method: refined / Origin x: -5.1636 Å / Origin y: -1.5053 Å / Origin z: 85.7442 Å
111213212223313233
T0.0868 Å2-0.0018 Å20.0047 Å2-0.0883 Å2-0.0013 Å2--0.0905 Å2
L0.6152 °2-0.0012 °20.1596 °2-0.6074 °2-0.0652 °2--0.6544 °2
S-0.0152 Å °-0.0179 Å °0.013 Å °-0.033 Å °0.0188 Å °0.0005 Å °0.0023 Å °0.0177 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 - 255
4X-RAY DIFFRACTION1allD256 - 269
5X-RAY DIFFRACTION1allC1
6X-RAY DIFFRACTION1allC2
7X-RAY DIFFRACTION1allE1

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