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- PDB-6eku: Vibrio cholerae neuraminidase complexed with zanamivir -

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Basic information

Entry
Database: PDB / ID: 6eku
TitleVibrio cholerae neuraminidase complexed with zanamivir
ComponentsSialidase
KeywordsHYDROLASE / sialidase / bacterial protein / infection
Function / homology
Function and homology information


sialic acid binding / exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / extracellular region ...sialic acid binding / exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
Vibrio cholerae neuraminidase, lectin-like domain / Vibrio cholerae sialidase, lectin insertion / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 ...Vibrio cholerae neuraminidase, lectin-like domain / Vibrio cholerae sialidase, lectin insertion / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / ZANAMIVIR / Sialidase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchuetz, A. / Heinemann, U.
CitationJournal: Molecules / Year: 2017
Title: Different Inhibitory Potencies of Oseltamivir Carboxylate, Zanamivir, and Several Tannins on Bacterial and Viral Neuraminidases as Assessed in a Cell-Free Fluorescence-Based Enzyme Inhibition Assay.
Authors: Quosdorf, S. / Schuetz, A. / Kolodziej, H.
History
DepositionSep 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,93210
Polymers83,0391
Non-polymers8939
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-17 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.553, 50.344, 86.087
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1321-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sialidase / Neuraminidase / NANase


Mass: 83039.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: nanH, VC_1784 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6E9, exo-alpha-sialidase
#2: Sugar ChemComp-ZMR / ZANAMIVIR / 4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / 4-guanidino-Neu5Ac2en / MODIFIED SIALIC ACID


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication, inhibitor*YM

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Non-polymers , 5 types, 668 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2 M sodium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.75→46 Å / Num. obs: 77459 / % possible obs: 97.8 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.66
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 7630 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KIT

1kit


Resolution: 1.75→46 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2029 3872 5 %
Rwork0.1669 --
obs0.1687 77422 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5841 0 57 660 6558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076031
X-RAY DIFFRACTIONf_angle_d1.0498206
X-RAY DIFFRACTIONf_dihedral_angle_d14.0292188
X-RAY DIFFRACTIONf_chiral_restr0.047904
X-RAY DIFFRACTIONf_plane_restr0.0051084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7492-1.77050.33771300.32992472X-RAY DIFFRACTION94
1.7705-1.79290.33661410.31362679X-RAY DIFFRACTION98
1.7929-1.81650.32021370.29642596X-RAY DIFFRACTION98
1.8165-1.84140.32681380.28162623X-RAY DIFFRACTION99
1.8414-1.86770.30611380.26022625X-RAY DIFFRACTION98
1.8677-1.89560.24081370.24182587X-RAY DIFFRACTION98
1.8956-1.92520.2831380.23832640X-RAY DIFFRACTION97
1.9252-1.95680.22481360.21362596X-RAY DIFFRACTION98
1.9568-1.99050.2821370.20052604X-RAY DIFFRACTION98
1.9905-2.02670.2561410.19232664X-RAY DIFFRACTION99
2.0267-2.06570.25411350.19022575X-RAY DIFFRACTION98
2.0657-2.10790.20871360.18752589X-RAY DIFFRACTION96
2.1079-2.15370.23251380.19192618X-RAY DIFFRACTION98
2.1537-2.20380.23041390.18622635X-RAY DIFFRACTION98
2.2038-2.25890.24231350.18382571X-RAY DIFFRACTION97
2.2589-2.320.20131400.18522655X-RAY DIFFRACTION98
2.32-2.38830.22281400.17172646X-RAY DIFFRACTION98
2.3883-2.46530.23381370.17182606X-RAY DIFFRACTION98
2.4653-2.55350.23011390.16932637X-RAY DIFFRACTION99
2.5535-2.65570.21011390.16522656X-RAY DIFFRACTION98
2.6557-2.77650.23531380.16882616X-RAY DIFFRACTION97
2.7765-2.92290.20881410.16642673X-RAY DIFFRACTION99
2.9229-3.1060.19381390.15592635X-RAY DIFFRACTION98
3.106-3.34570.191400.15432677X-RAY DIFFRACTION99
3.3457-3.68230.19831400.14612644X-RAY DIFFRACTION97
3.6823-4.21480.14471390.12982643X-RAY DIFFRACTION97
4.2148-5.3090.1321410.11192687X-RAY DIFFRACTION98
5.309-46.0170.16031430.1462701X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7424-0.7747-0.02741.5325-0.73363.4291-0.0004-0.029-0.064-0.0319-0.0798-0.18030.34360.39450.0710.22930.0599-0.01310.4224-0.02290.203218.8651-0.392332.4456
21.9966-0.06570.56090.1499-0.03041.1350.1490.5671-0.1182-0.0656-0.0911-0.04080.11640.4096-0.06690.20520.0583-0.01590.4196-0.06520.1852-13.70851.93986.2321
32.13370.01520.13751.174-0.60191.87450.0349-0.12090.15930.12620.04590.2355-0.045-0.1883-0.07090.16470.01670.01990.1413-0.00890.2398-51.801312.42639.8242
42.188-0.00790.59590.5268-0.02251.3428-0.0115-0.03690.10570.0469-0.0231-0.0222-0.02850.15740.03450.1502-0.0012-0.00270.2094-0.01170.1178-16.59111.890922.9272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 380 )
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 567 )
4X-RAY DIFFRACTION4chain 'A' and (resid 568 through 804 )

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