[English] 日本語
Yorodumi
- PDB-7e6q: Crystal structure of influenza A virus neuraminidase N5 complexed... -

+
Open data


ID or keywords:

Loading...

-
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-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more