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- PDB-1inf: INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE COMPLEXED WITH BANA113 INH... -

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Basic information

Entry
Database: PDB / ID: 1inf
TitleINFLUENZA VIRUS B/LEE/40 NEURAMINIDASE COMPLEXED WITH BANA113 INHIBITOR
ComponentsINFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
KeywordsHYDROLASE (O-GLYCOSYL) / NEURAMINIDASE / SIALIDASE / HYDROLASE / O-GLYCOSYL
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
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
4-(ACETYLAMINO)-3-GUANIDINOBENZOIC ACID / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsJedrzejas, M.J. / Luo, M.
Citation
Journal: J.Med.Chem. / Year: 1995
Title: Structure-based inhibitors of influenza virus sialidase. A benzoic acid lead with novel interaction.
Authors: Singh, S. / Jedrzejas, M.J. / Air, G.M. / Luo, M. / Laver, W.G. / Brouillette, W.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Benzoic Acid Inhibitors of Influenza Virus Neuraminidase
Authors: Luo, M. / Jedrzejas, M.J. / Singh, S. / White, C.L. / Brouillette, W.J. / Air, G.M. / Laver, W.G.
#2: Journal: J.Med.Chem. / Year: 1995
Title: Structure-Based Inhibitors of Influenza Viral Neuraminidase. A Benzoic Acid Lead with Novel Interaction
Authors: Singh, S. / Jedrzejas, M.J. / Air, G.M. / Luo, M. / Laver, W.G. / Brouillette, W.J.
#3: Journal: Biochemistry / Year: 1995
Title: Structures of Aromatic Inhibitors of Influenza Virus Neuraminidase
Authors: Jedrzejas, M.J. / Singh, S. / Brouillette, W.J. / Laver, W.G. / Air, G.M. / Luo, M.
#4: Journal: Biochemistry / Year: 1994
Title: Structure of Influenza Virus Neuraminidase B/Lee/40 Complexed with Sialic Acid and a Dehydro Analog at 1.8-A Resolution: Implications for the Catalytic Mechanism
Authors: Janakiraman, M.N. / White, C.L. / Laver, W.G. / Air, G.M. / Luo, M.
#5: Journal: J.Mol.Biol. / Year: 1991
Title: Three-Dimensional Structure of the Neuraminidase of Influenza Virus A/Tokyo/3/67 at 2.2 A Resolution
Authors: Varghese, J.N. / Colman, P.M.
#6: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants
Authors: Tulip, W.R. / Varghese, J.N. / Baker, A.T. / Van Donkelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M.
History
DepositionJul 7, 1995Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.name ..._atom_site.occupancy / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9725
Polymers43,4321
Non-polymers5404
Water2,234124
1
A: INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
hetero molecules

A: INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
hetero molecules

A: INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
hetero molecules

A: INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,88820
Polymers173,7294
Non-polymers2,15816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area19010 Å2
ΔGint-108 kcal/mol
Surface area45750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.250, 124.250, 71.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-501-

CA

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Components

#1: Protein INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE / SIALIDASE


Mass: 43432.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza B virus / Genus: Influenzavirus B / Strain: STRAIN B-LEE-40 / References: UniProt: P03474, 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ST4 / 4-(ACETYLAMINO)-3-GUANIDINOBENZOIC ACID


Mass: 238.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Lin, Y., (1990) J. Mol. Biol., 214, 639.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 %(v/v)PEG40001drop
20.01 MHEPES1droppH7.4
310 mM1dropNaNO3
42.5 mM1dropCaCl2
530 %(v/v)PEG40001reservoir
60.02 MHEPES1reservoirpH7.4

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 22, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 17683 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.125
Reflection
*PLUS
Highest resolution: 1.9 Å

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Processing

Software
NameVersionClassification
XENGENdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.4→6.5 Å / σ(F): 4
Details: THE REFINED MODEL COORDINATES DEPOSITED CONTAIN THE FULL PROTEIN SEQUENCE FROM GLU 77 TO LEU 466. THE TWO CALCIUM ATOMS ARE INCLUDED IN THE REFINED STRUCTURE. RESIDUE CA 500 STABILIZES A ...Details: THE REFINED MODEL COORDINATES DEPOSITED CONTAIN THE FULL PROTEIN SEQUENCE FROM GLU 77 TO LEU 466. THE TWO CALCIUM ATOMS ARE INCLUDED IN THE REFINED STRUCTURE. RESIDUE CA 500 STABILIZES A LOOP NEAR THE NEURAMINIDASE ACTIVE SITE, WHILE CA 501 IS LOCATED ON THE CRYSTALLOGRAPHIC NEURAMINIDASE TETRAMER FOUR-FOLD AXIS. THE EQUATORIAL PHOSPHONATE INHIBITOR IS RESIDUE EQP 500.
RfactorNum. reflection
Rwork0.159 -
obs0.159 16494
Refinement stepCycle: LAST / Resolution: 2.4→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 33 124 3195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.92
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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