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- PDB-1inv: A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAI... -

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Entry
Database: PDB / ID: 1inv
TitleA SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAINS OF INFLUENZA VIRUS NEURAMINIDASE WITH DIFFERENT EFFICIENCIES
ComponentsINFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
KeywordsHYDROLASE / O-GLYCOSYL / NEURAMINIDASE / SIALIDASE
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
Chem-EQP / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsWhite, C.L. / Janakiraman, M.N. / Laver, W.G. / Philippon, C. / Vasella, A. / Air, G.M. / Luo, M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies.
Authors: White, C.L. / Janakiraman, M.N. / Laver, W.G. / Philippon, C. / Vasella, A. / Air, G.M. / Luo, M.
#1: Journal: Biochemistry / Year: 1994
Title: Structure of Influenza Virus Neuraminidase B(Slash)Lee(Slash)40 Complexed with Sialic Acid and a Dehydro Analog at 1.8 Angstroms Resolution: Implications for the Catalytic Mechanism
Authors: Janakiraman, M.N. / White, C.L. / Laver, W.G. / Air, G.M. / Luo, M.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Three-Dimensional Structure of the Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution
Authors: Varghese, J.N. / Colman, P.M.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants
Authors: Lip, W.R. / Varghese, J.N. / Baker, A.T. / Van Danelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M.
#4: Journal: Helv.Chim.Acta / Year: 1990
Title: Phosphonic-Acid Analogs of the N-Acetyl-2-Deoxyneuraminic Acids: Synthesis and Inhibition of Vibrio Choleae Sialidase
Authors: Walliman, K. / Vasella, A.
History
DepositionSep 26, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 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 ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,0915
Polymers43,4601
Non-polymers6314
Water2,108117
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)176,36420
Polymers173,8414
Non-polymers2,52216
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 area19480 Å2
ΔGint-123 kcal/mol
Surface area45970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.730, 124.730, 71.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Atom site foot note1: CIS PROLINE - PRO 139 / 2: CIS PROLINE - PRO 326
Components on special symmetry positions
IDModelComponents
11A-469-

CA

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Components

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


Mass: 43460.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Genus: Influenzavirus B / Cell line: 293 / Strain (production host): 293 / 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: Sugar ChemComp-EQP / (1R)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol / (4-ACETAMIDO-2,4-DIDEOXY-D-GLYCERO-ALPHA-D-GALACTO-1-OCTOPYRANOSYL)PHOSPHONIC ACID


Type: D-saccharide / Mass: 329.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20NO9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTWO CALCIUMS ATOMS ARE INCLUDED IN THE REFINED STRUCTURE. RESIDUE CA 467 STABILIZES A LOOP NEAR THE ...TWO CALCIUMS ATOMS ARE INCLUDED IN THE REFINED STRUCTURE. RESIDUE CA 467 STABILIZES A LOOP NEAR THE NEURAMINIDASE ACTIVE SITE, WHILE CA 468 IS LOCATED ON THE CRYSTALLOGRAPHIC NEURAMINIDASE TETRAMER FOUR-FOLD AXIS. THE EQUATORIAL PHOSPHONATE INHIBITOR IS RESIDUE EQP 500. EQP IS AN EQUATORIAL PHOSPHONATE ANALOG OF O-SIALIC ACID.
Source detailsEPANA SEE WALLIMAN & VASELLA (1990) FOR SYNTHESIS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.74 %
Crystal growDetails: NATIVE CRYSTALS SOAKED IN 10MM EPANA SOLUTION, PH 7.4.
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.01 MHEPES1reservoir
22 M1reservoirNaNO3
35 mM1reservoirCa2+
415 %(w/v)PEG33501reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 17019 / % possible obs: 72.3 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2.38 Å / Lowest resolution: 9999 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.0967

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.154 -
obs0.154 16341
Displacement parametersBiso mean: 13.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 37 117 3194
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_deg1.77
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.88
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.45
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.154 / Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.77
X-RAY DIFFRACTIONx_dihedral_angle_d26.9

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