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- PDB-7e6q: Crystal structure of influenza A virus neuraminidase N5 complexed... -

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Basic information

Entry
Database: PDB / ID: 7e6q
TitleCrystal structure of influenza A virus neuraminidase N5 complexed with 4'-phenyl-1,2,3-triazolylated oseltamivir carboxylate
ComponentsNeuraminidase
KeywordsHYDROLASE / Influenza virus / Neuraminidase inhibitors / Oseltamivir derivatives / 150-cavity
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Chem-HZF / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, P.F. / Babayemi, O.O. / Li, C.N. / Fu, L.F. / Zhang, S.S. / Qi, J.X. / Lv, X. / Li, X.B.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Rsc Adv / Year: 2021
Title: Structure-based design of 5'-substituted 1,2,3-triazolylated oseltamivir derivatives as potent influenza neuraminidase inhibitors.
Authors: Wang, P. / Oladejo, B.O. / Li, C. / Fu, L. / Zhang, S. / Qi, J. / Lv, X. / Li, X.
History
DepositionFeb 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6339
Polymers87,0642
Non-polymers1,5697
Water1,40578
1
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4275
Polymers43,5321
Non-polymers8954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-6 kcal/mol
Surface area15150 Å2
MethodPISA
2
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2064
Polymers43,5321
Non-polymers6743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-10 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.064, 109.064, 71.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Space group name HallP4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z

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Components

#1: Protein Neuraminidase /


Mass: 43531.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Alberta/60/1976 H12N5)
Strain: A/Duck/Alberta/60/1976 H12N5 / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A1ILL9, exo-alpha-sialidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-HZF / (3R,4R,5S)-4-acetamido-3-pentan-3-yloxy-5-(4-phenyl-1,2,3-triazol-1-yl)cyclohexene-1-carboxylic acid


Mass: 412.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 12% w/v Polyethylene glycol 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 42631 / % possible obs: 95.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.235 / Num. unique obs: 40762

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SAN

3san


Resolution: 2.2→32.37 Å / SU ML: 0.2138 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 34.0087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 2064 5.07 %
Rwork0.207 38649 -
obs0.2085 40713 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 104 78 6266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00856342
X-RAY DIFFRACTIONf_angle_d1.21528607
X-RAY DIFFRACTIONf_chiral_restr0.0693929
X-RAY DIFFRACTIONf_plane_restr0.00631109
X-RAY DIFFRACTIONf_dihedral_angle_d17.92542254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.32531160.29152157X-RAY DIFFRACTION80.66
2.25-2.310.33241070.2732249X-RAY DIFFRACTION82.84
2.31-2.370.29221490.26872293X-RAY DIFFRACTION85.86
2.37-2.440.34751260.26072417X-RAY DIFFRACTION90.66
2.44-2.520.36341430.26932530X-RAY DIFFRACTION94.55
2.52-2.610.28521500.26452638X-RAY DIFFRACTION98.52
2.61-2.710.29831380.25172676X-RAY DIFFRACTION99.36
2.71-2.830.27971490.24412686X-RAY DIFFRACTION99.51
2.83-2.980.30731500.23272663X-RAY DIFFRACTION99.72
2.98-3.170.20251380.23252705X-RAY DIFFRACTION99.93
3.17-3.410.26191280.21462716X-RAY DIFFRACTION99.82
3.41-3.760.22421260.19512723X-RAY DIFFRACTION99.89
3.76-4.30.17951430.16112697X-RAY DIFFRACTION99.79
4.3-5.410.15791660.14322712X-RAY DIFFRACTION99.86
5.42-32.370.18171350.18052787X-RAY DIFFRACTION99.52
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)
10.894632189214-0.0245031170322-0.06099470547430.6707879934470.0047781774940.230258487994-0.008117249333890.0296751147043-0.0389403091641-0.01105916131760.000369881564617-0.1721655174240.01044743682770.02154698077730.009360361216570.218961556346-0.00265714135206-0.0121046730620.235648449666-0.005741790611890.288275172061137.02547735106.063166701-22.3872720608
20.81631134593-0.111312458149-0.1279258970830.531352803239-0.274001999670.359623549983-0.0750130467033-0.1329286491590.2820181205670.177194802624-0.0324471376814-0.0868722447472-0.0644182045869-0.04536713238320.09309548748390.3621332078150.0125622684372-0.06340474754210.351527663896-0.1111918211850.316898882487162.34787580982.79034941817.76032561103
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 82 - 982 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11chain AAA - E
22chain BBF - I

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