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- PDB-1ive: STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE -

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Basic information

Entry
Database: PDB / ID: 1ive
TitleSTRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE
ComponentsINFLUENZA A SUBTYPE N2 NEURAMINIDASE
KeywordsHYDROLASE (O-GLYCOSYL)
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
4-(ACETYLAMINO)-3-AMINO BENZOIC ACID / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A 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. / Singh, S. / Air, G.M. / Luo, M. / Laver, W.G. / Brouillette, W.J.
#2: Journal: To be Published
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.
#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.
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: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INFLUENZA A SUBTYPE N2 NEURAMINIDASE
B: INFLUENZA A SUBTYPE N2 NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,05914
Polymers86,2822
Non-polymers5,77712
Water0
1
A: INFLUENZA A SUBTYPE N2 NEURAMINIDASE
B: INFLUENZA A SUBTYPE N2 NEURAMINIDASE
hetero molecules

A: INFLUENZA A SUBTYPE N2 NEURAMINIDASE
B: INFLUENZA A SUBTYPE N2 NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,11928
Polymers172,5644
Non-polymers11,55524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)121.880, 140.880, 141.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: TYR 284 - PRO 285 OMEGA = 215.65 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO 326
3: ASP 329 - ASP 330 OMEGA = 210.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: THR 385 - PRO 386 OMEGA = 216.37 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: ARG 430 - LYS 431 OMEGA = 233.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (-1))
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 82 .. 469 ..

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein INFLUENZA A SUBTYPE N2 NEURAMINIDASE


Mass: 43141.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Tokyo/3/1967 H2N2)
Strain: A/Tokyo/3/1967 H2N2 / References: UniProt: P06820, exo-alpha-sialidase

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Sugars , 5 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 4 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-ST3 / 4-(ACETYLAMINO)-3-AMINO BENZOIC ACID


Mass: 194.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10N2O3

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Details

Nonpolymer detailsTHE CALCIUM, CA 470, STABILIZES A LOOP NEAR THE NEURAMINIDASE ACTIVE SITE. THE BANA108 INHIBITOR IS ...THE CALCIUM, CA 470, STABILIZES A LOOP NEAR THE NEURAMINIDASE ACTIVE SITE. THE BANA108 INHIBITOR IS RESIDUE ST3 471.
Source detailsMOLECULE_NAME: BANA108 SYNTHETIC. SEE SINGH ET AL. (SUBMITTED TO J. MED CHEM.) AND JEDRZEJAS ET AL. ...MOLECULE_NAME: BANA108 SYNTHETIC. SEE SINGH ET AL. (SUBMITTED TO J. MED CHEM.) AND JEDRZEJAS ET AL. (ACCEPTED BY BIOCHEMISTRY, 1994) FOR SYNTHESIS INFORMATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growDetails: NATIVE CRYSTALS SOAKED IN 5MM BANA108 SOLUTION, PH 6.8.
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 25898 / Observed criterion σ(I): 1
Reflection
*PLUS
Rmerge(I) obs: 0.093

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→6.5 Å / σ(F): 4
Details: ONLY HALF OF THE ASYMMETRIC UNIT WAS REFINED; THE REMAINING HALF WAS GENERATED USING A NONCRYSTALLOGRAPHIC TWO-FOLD AXIS. THE TOPOLOGY AND PARAMETER VALUES GENERATED FOR THE BANA108 RESIDUES ...Details: ONLY HALF OF THE ASYMMETRIC UNIT WAS REFINED; THE REMAINING HALF WAS GENERATED USING A NONCRYSTALLOGRAPHIC TWO-FOLD AXIS. THE TOPOLOGY AND PARAMETER VALUES GENERATED FOR THE BANA108 RESIDUES WERE EITHER TAKEN DIRECTLY FROM THE LITERATURE OR BY COMPARISON TO OTHER SIMILAR STRUCTURES IN THE X-PLOR TOPOLOGY AND PARAMETER LIBRARY FILES. MORE INFORMATION CONCERNING THE REFINEMENT PROTOCOLS AND BANA108 FILES IS PRESENTED IN THE ORIGINATING PAPER.
RfactorNum. reflection
Rwork0.217 -
obs0.217 23218
Refinement stepCycle: LAST / Resolution: 2.4→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 384 0 6428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.701
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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