[English] 日本語
Yorodumi
- PDB-1ivb: STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ivb
TitleSTRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE
ComponentsINFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / 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
4-(ACETYLAMINO)-3-HYDROXY-5-NITROBENZOIC ACID / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsJedrzejas, M.J. / Luo, M.
Citation
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.
#1: Journal: To be Published
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.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution
Authors: Varghese, J.N. / Colman, P.M.
#4: 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
DepositionDec 12, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...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: _chem_comp.name / _chem_comp.type ..._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_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_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 1.4Oct 23, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,0025
Polymers43,4601
Non-polymers5424
Water00
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)176,00820
Polymers173,8414
Non-polymers2,16616
Water0
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 area18500 Å2
ΔGint-98 kcal/mol
Surface area46240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.540, 124.540, 71.820
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-501-

CA

-
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 / 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-ST1 / 4-(ACETYLAMINO)-3-HYDROXY-5-NITROBENZOIC ACID


Mass: 240.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2O6
Has protein modificationY
Nonpolymer detailsTWO CALCIUMS ATOMS ARE INCLUDED IN THE REFINED STRUCTURE. CA 500 STABILIZES A LOOP NEAR THE ...TWO CALCIUMS ATOMS ARE INCLUDED IN THE REFINED STRUCTURE. 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.
Source detailsMOLECULE_NAME: BANA105 SYNTHETIC. SEE SINGH ET AL. (SUBMITTED TO J. MED CHEM.) AND JEDRZEJAS ET AL. ...MOLECULE_NAME: BANA105 SYNTHETIC. SEE SINGH ET AL. (SUBMITTED TO J. MED CHEM.) AND JEDRZEJAS ET AL. (ACCEPTED BY BIOCHEMISTRY, 1994) FOR SYNTHESIS INFORMATION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growDetails: NATIVE CRYSTALS SOAKED IN 5MM BANA105 SOLUTION, PH 7.4.
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Lin, Y., (1990) J. Mol. Biol., 214, 639.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %(v/v)PEG40001drop
20.01 MHEPES1drop
310 mM1dropNaNO3
42.5 mM1dropCaCl2
520 %(v/v)PEG40001reservoir
60.02 MHEPES1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 15271 / Observed criterion σ(I): 1
Reflection
*PLUS
Rmerge(I) obs: 0.104

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→6.5 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.189 -
obs0.189 14129
Refinement stepCycle: LAST / Resolution: 2.4→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 33 0 3073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.142
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
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.142

+
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