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- PDB-4ks5: Influenza neuraminidase in complex with antiviral compound (3S,4R... -

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Basic information

Entry
Database: PDB / ID: 4ks5
TitleInfluenza neuraminidase in complex with antiviral compound (3S,4R,5R)-4-(acetylamino)-3-[4-(2-hydroxypropan-2-yl)-1H-1,2,3-triazol-1-yl]-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Sialidase / HYDROLASE-HYDROLASE INHIBITOR complex
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 / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-1SO / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.699 Å
AuthorsKerry, P.S. / Russell, R.J.M.
CitationJournal: Sci Rep / Year: 2013
Title: Structural basis for a class of nanomolar influenza A neuraminidase inhibitors.
Authors: Kerry, P.S. / Mohan, S. / Russell, R.J. / Bance, N. / Niikura, M. / Pinto, B.M.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6313
Polymers43,1971
Non-polymers4352
Water1,13563
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,52512
Polymers172,7874
Non-polymers1,7388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area13460 Å2
ΔGint-76 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.279, 90.279, 94.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Neuraminidase


Mass: 43196.664 Da / Num. of mol.: 1 / Fragment: UNP residues 81-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Duck/Ukraine/1/1963 H3N8 / Gene: NA / Production host: Escherichia coli (E. coli) / References: UniProt: Q0A480
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-1SO / (3S,4R,5R)-4-(acetylamino)-3-[4-(2-hydroxypropan-2-yl)-1H-1,2,3-triazol-1-yl]-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid


Mass: 394.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30N4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 40% 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twinOperator: -h,k,-l / Fraction: 0.46
ReflectionResolution: 2.699→65.3 Å / Num. all: 10536 / Num. obs: 10514 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.185

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HT5

2ht5


Resolution: 2.699→38.025 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.41 / Phase error: 22.37 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1977 1036 9.88 %
Rwork0.1682 --
obs0.172 10489 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.2246 Å2
Refinement stepCycle: LAST / Resolution: 2.699→38.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 29 63 3101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143125
X-RAY DIFFRACTIONf_angle_d1.264233
X-RAY DIFFRACTIONf_dihedral_angle_d14.3621113
X-RAY DIFFRACTIONf_chiral_restr0.088449
X-RAY DIFFRACTIONf_plane_restr0.006548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-2.84310.25031560.2151353X-RAY DIFFRACTION89
2.8431-3.02080.26211400.20721321X-RAY DIFFRACTION90
3.0208-3.25330.21461520.18651331X-RAY DIFFRACTION89
3.2533-3.57940.18451580.1631330X-RAY DIFFRACTION89
3.5794-4.09440.18941440.14571338X-RAY DIFFRACTION90
4.0944-5.14730.17881420.14191352X-RAY DIFFRACTION90
5.1473-21.77980.1781420.1741388X-RAY DIFFRACTION91

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