1IVB - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE

Authors :   M. J. Jedrzejas, M. Luo

Date :   12 Dec 94 (Deposition) - 31 Mar 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Hydrolase (O-Glycosyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Jedrzejas, S. Singh, W. J. Brouillette, W. G. Laver, G. M. Air, M. Luo
Structures Of Aromatic Inhibitors Of Influenza Virus Neuraminidase.
Biochemistry V. 34 3144 1995
PubMed-ID: 7880809 | Reference-DOI: 10.1021/BI00010A003
(for further references see the PDB file header)

Molecule 1 - INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE
	Chains	:	A
	EC Number	:	3.2.1.18
	Engineered	:	YES
	Organism Scientific	:	INFLUENZA B VIRUS
	Organism Taxid	:	11520

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	ST1	1	Ligand/Ion	4-(ACETYLAMINO)-3-HYDROXY-5-NITROBENZOIC ACID

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	ST1	4	Ligand/Ion	4-(ACETYLAMINO)-3-HYDROXY-5-NITROBENZOIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:82 , PRO A:83 , ARG A:84 , ASN A:284	BINDING SITE FOR RESIDUE NAG A 467
2	AC2	SOFTWARE	ASP A:293 , THR A:297 , ASP A:324 , TRP A:344 , GLY A:346	BINDING SITE FOR RESIDUE CA A 500
3	AC3	SOFTWARE	GLU A:168	BINDING SITE FOR RESIDUE CA A 501
4	AC4	SOFTWARE	ARG A:116 , GLU A:117 , ASP A:149 , ARG A:150 , ILE A:221 , ARG A:223 , GLU A:276 , ARG A:292 , ARG A:374 , TYR A:409	BINDING SITE FOR RESIDUE ST1 A 471
5	CAT	AUTHOR	ARG A:116 , GLU A:117 , ASP A:149 , ARG A:150 , TRP A:177 , ILE A:221 , ARG A:223 , GLU A:275 , ARG A:292 , ARG A:374 , TYR A:409	SUBSTRATE (SIALIC ACID) BINDING RESIDUES IN CATALYTIC SITE

Asymmetric Unit

No.	Residues
1	A:87	-	A:420
2	A:122	-	A:127
3	A:182	-	A:229
4	A:231	-	A:236
5	A:277	-	A:291
6	A:279	-	A:289
7	A:318	-	A:337
8	A:424	-	A:447

Asymmetric Unit

No.	Residues
1	Gln A:138	-	Pro A:139
2	Thr A:325	-	Pro A:326

(no "SAP(SNP)/Variant" information available for 1IVB)

(no "PROSITE Motif" information available for 1IVB)

(no "Exon" information available for 1IVB)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:390
 aligned with NRAM_INBLE | P03474 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:390
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466
           NRAM_INBLE    77 EPEWTYPRLSCQGSTFQKALLISPHRFGEIKGNSAPLIIREPFVACGPKECRHFALTHYAAQPGGYYNGTRKDRNKLRHLVSVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDNDALVKIKYGEAYTDTYHSYAHNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEILPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTKTYLDTPRPDDGSIAGPCESNGDKWLGGIKGGFVHQRMASKIGRWYSRTMSKTNRMGMELYVKYDGDPWTDSDALTLSGVMVSIEEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKDTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 466
               SCOP domains d1ivba_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ivbA00 A:77-466  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeeeee.hhhh...............eeee....eeeeeee.....................eeeeee..........eeeee..eeeeee....eeeeeeeee..eeeeeeee..eeeeeee..............eee..eeeeee...........eeeee....eeeeee...........eeee....eeeee..........eeeeee....eeeeee...................................eeeee....eeeeeee..........eeeeee..........................eeeeeee....eeeeeeeeeeee......eeeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ivb A  77 EPEWTYPRLSCQGSTFQKALLISPHRFGEIKGNSAPLIIREPFVACGPKECRHFALTHYAAQPGGYYNGTRKDRNKLRHLVSVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDNDALVKIKYGEAYTDTYHSYAHNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEILPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTKTYLDTPRPDDGSIAGPCESNGDKWLGGIKGGFVHQRMASKIGRWYSRTMSKTNRMGMELYVRYDGDPWTDSDALTLSGVMVSIEEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKDTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 466
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: Sialidases (238)

Family: Sialidases (neuraminidases) (178)

Protein domain: Influenza neuraminidase (78)

Influenza B virus, different strains [TaxId: 11520] (17)

d1ivba_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 6 Propellor (215)

Topology: Neuraminidase (215)

Homologous Superfamily: [code=2.120.10.10, no name defined] (150)

Influenza b virus. Organism_taxid: 11520 (1)

1ivbA00

A:77-466

(no "Pfam Domain" information available for 1IVB)

Asymmetric Unit(hide GO term definitions)

Chain A (NRAM_INBLE | P03474)

molecular function
	GO:0052794	exo-alpha-(2->3)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052795	exo-alpha-(2->6)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052796	exo-alpha-(2->8)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0004308	exo-alpha-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		Gln A:138 - Pro A:139	[ RasMol ]
		Thr A:325 - Pro A:326	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (5, 5)

SS Bonds (8, 8)

Cis Peptide Bonds (2, 2)

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