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- PDB-1a4q: INFLUENZA VIRUS B/BEIJING/1/87 NEURAMINIDASE COMPLEXED WITH DIHYD... -

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Basic information

Entry
Database: PDB / ID: 1a4q
TitleINFLUENZA VIRUS B/BEIJING/1/87 NEURAMINIDASE COMPLEXED WITH DIHYDROPYRAN-PHENETHYL-PROPYL-CARBOXAMIDE
ComponentsNEURAMINIDASE
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOSYLATED PROTEIN
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 / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-DPC / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.9 Å
AuthorsCleasby, A. / Singh, O. / Skarzynski, T. / Wonacott, A.J.
Citation
Journal: J.Med.Chem. / Year: 1998
Title: Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6- ...Title: Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6-carboxamides and sialidase from influenza virus types A and B.
Authors: Taylor, N.R. / Cleasby, A. / Singh, O. / Skarzynski, T. / Wonacott, A.J. / Smith, P.W. / Sollis, S.L. / Howes, P.D. / Cherry, P.C. / Bethell, R. / Colman, P. / Varghese, J.
#1: Journal: Embo J. / Year: 1992
Title: The 2.2 A Resolution Crystal Structure of Influenza B Neuraminidase and its Complex with Sialic Acid
Authors: Burmeister, W.P. / Ruigrok, R.W. / Cusack, S.
#2: Journal: Virology / Year: 1991
Title: Sequence and Crystallization of Influenza Virus B/Beijing/1/87 Neuraminidase
Authors: Burmeister, W.P. / Daniels, R.S. / Dayan, S. / Gagnon, J. / Cusack, S. / Ruigrok, R.W.
History
DepositionJan 30, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / 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: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2009
Polymers86,8592
Non-polymers1,3427
Water8,953497
1
A: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
B: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,40018
Polymers173,7174
Non-polymers2,68314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area20670 Å2
ΔGint-137 kcal/mol
Surface area45610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.300, 88.300, 221.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.25, 0.433, -0.866), (0.433, 0.75, 0.5), (0.866, -0.5))

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Components

#1: Protein NEURAMINIDASE / / SIALIDASE


Mass: 43429.254 Da / Num. of mol.: 2 / Fragment: RESIDUES 76-465 / Source method: isolated from a natural source / Source: (natural) Influenza B virus (STRAIN B/BEIJING/1/87) / Genus: Influenzavirus BInfluenza B virus / Species: Influenza B virus / Strain: B/Beijing/1/87 / References: UniProt: P27907, exo-alpha-sialidase
#2: 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.: 2
Source method: isolated from a genetically manipulated source
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-DPC / 5-ACETYLAMINO-4-AMINO-6-(PHENETHYL-PROPYL-CARBAMOYL)-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC ACID


Type: L-saccharide / Mass: 389.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H27N3O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Method: seeding / PH range low: 8 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 %PEG800011
2100 mMTris-HCl11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1995 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→34 Å / Num. obs: 208669 / % possible obs: 97.4 % / Observed criterion σ(I): 5 / Redundancy: 2.7 % / Rmerge(I) obs: 0.092
Reflection
*PLUS
Num. obs: 77084 / Num. measured all: 208669

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.8model building
X-PLOR3.8refinement
CCP4data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1NSC

1nsc


Resolution: 1.9→34 Å
Details: THE TWO MONOMERS IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT HAVE BEEN REFINED INDEPENDENTLY.
RfactorNum. reflection
Rwork0.201 -
obs0.201 77031
Refinement stepCycle: LAST / Resolution: 1.9→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 87 497 6656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it3
X-RAY DIFFRACTIONx_scbond_it2.7
X-RAY DIFFRACTIONx_scangle_it4
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.286 8601 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ENGH.PROTOPENGH.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16
LS refinement shell
*PLUS
Rfactor obs: 0.286

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