1A4G - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   INFLUENZA VIRUS B/BEIJING/1/87 NEURAMINIDASE COMPLEXED WITH ZANAMIVIR

Authors :   A. Cleasby, O. Singh, T. Skarzynski, A. J. Wonacott

Date :   29 Jan 98 (Deposition) - 02 Mar 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Hydrolase, Glycosidase, Glycosylated Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. R. Taylor, A. Cleasby, O. Singh, T. Skarzynski, A. J. Wonacott, P. W. Smith, S. L. Sollis, P. D. Howes, P. C. Cherry, R. Bethell, P. Colman, J. Varghese
Dihydropyrancarboxamides Related To Zanamivir: A New Series Of Inhibitors Of Influenza Virus Sialidases. 2. Crystallographic And Molecular Modeling Study Of Complexes Of 4-Amino-4H-Pyran-6-Carboxamides And Sialidase From Influenza Virus Types A And B.
J. Med. Chem. V. 41 798 1998
PubMed-ID: 9526556 | Reference-DOI: 10.1021/JM9703754
(for further references see the PDB file header)

Molecule 1 - NEURAMINIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.18
	Fragment	:	RESIDUES 76-465
	Organism Scientific	:	INFLUENZA B VIRUS (STRAIN B/BEIJING/1/87)
	Organism Taxid	:	11525
	Strain	:	B/BEIJING/1/87
	Synonym	:	SIALIDASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	ZMR	2	Ligand/Ion	ZANAMIVIR

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	ZMR	4	Ligand/Ion	ZANAMIVIR

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:82 , ASN A:283 , HOH A:538 , HOH A:579 , HOH A:596 , HOH A:609 , HOH A:633	BINDING SITE FOR RESIDUE NAG A 1
02	AC2	SOFTWARE	PRO B:82 , ASN B:283 , HOH B:581 , HOH B:628 , HOH B:702	BINDING SITE FOR RESIDUE NAG B 1
03	AC3	SOFTWARE	ASP A:292 , THR A:296 , ASP A:323 , GLY A:343 , GLY A:345 , HOH A:594	BINDING SITE FOR RESIDUE CA A 2
04	AC4	SOFTWARE	ASP B:292 , THR B:296 , ASP B:323 , GLY B:343 , GLY B:345 , HOH B:551	BINDING SITE FOR RESIDUE CA B 2
05	AC5	SOFTWARE	ALA A:110 , ASN B:108 , SER B:109 , HOH B:480	BINDING SITE FOR RESIDUE CA B 3
06	AC6	SOFTWARE	ARG A:115 , GLU A:116 , ASP A:148 , ARG A:149 , ARG A:153 , TRP A:176 , ARG A:222 , GLU A:225 , ALA A:244 , GLU A:274 , ARG A:291 , ARG A:373 , TYR A:408 , HOH A:701 , HOH A:704 , HOH A:713	BINDING SITE FOR RESIDUE ZMR A 466
07	AC7	SOFTWARE	ARG B:115 , GLU B:116 , ASP B:148 , ARG B:149 , ARG B:153 , TRP B:176 , ILE B:220 , ARG B:222 , GLU B:225 , ALA B:244 , GLU B:274 , GLU B:275 , ARG B:291 , ASN B:293 , ARG B:373 , TYR B:408 , HOH B:685 , HOH B:686 , HOH B:694	BINDING SITE FOR RESIDUE ZMR B 466
08	CHA	UNKNOWN	ASP A:323 , GLY A:343 , GLY A:345 , THR A:296 , ASP A:292	HIGH AFFINITY CALCIUM BINDING SITE IN CHAIN A.
09	CHB	UNKNOWN	ASP B:323 , GLY B:343 , GLY B:345 , THR B:296 , ASP B:292	HIGH AFFINITY CALCIUM BINDING SITE IN CHAIN B.
10	CLA	UNKNOWN	GLU A:167	LOW AFFINITY CALCIUM BINDING SITE IN CHAIN A.
11	CLB	UNKNOWN	GLU B:167	N/LOW AFFINITY CALCIUM BINDING SITE IN CHAIN B.
12	ZAA	UNKNOWN	ASP A:323 , ARG A:115 , ARG A:291 , ARG A:149 , ILE A:220 , ARG A:222 , TRP A:176 , GLU A:274 , ASP A:148 , TYR A:408	BINDING SITE FOR ZANAMIVIR IN CHAIN A.
13	ZAB	UNKNOWN	ASP B:323 , ARG B:115 , ARG B:291 , ARG B:149 , ILE B:220 , ARG B:222 , TRP B:176 , GLU B:274 , ASP B:148 , TYR B:408	BINDING SITE FOR ZANAMIVIR IN CHAIN B.

Asymmetric Unit

No.	Residues
1	A:86	-	A:419
2	A:121	-	A:126
3	A:181	-	A:228
4	A:230	-	A:235
5	A:276	-	A:290
6	A:278	-	A:288
7	A:317	-	A:336
8	A:423	-	A:446
9	B:86	-	B:419
10	B:121	-	B:126
11	B:181	-	B:228
12	B:230	-	B:235
13	B:276	-	B:290
14	B:278	-	B:288
15	B:317	-	B:336
16	B:423	-	B:446

Asymmetric Unit

No.	Residues
1	Gln A:137	-	Pro A:138
2	Thr A:324	-	Pro A:325
3	Gln B:137	-	Pro B:138
4	Thr B:324	-	Pro B:325

(no "SAP(SNP)/Variant" information available for 1A4G)

(no "PROSITE Motif" information available for 1A4G)

(no "Exon" information available for 1A4G)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:390
 aligned with NRAM_INBBE | P27907 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:390
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465
           NRAM_INBBE    76 EPEWTYPRLSCQGSTFQKALLISPHRFGEARGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHSYANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASKIGRWYSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 465
               SCOP domains d1a4ga_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1a4gA00 A:76-465  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeeeee.hhhh..........eeeeeeeee....eeeeeee.....................eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee.......ee.....eee..eeeeeeeee.....eeeeeeeee..eeeeee.........eeeeeee....eeeeeee........eeeeee....eeeeee...................................eeeee....eeeeeee.........eeeeeee...........eeeeeee........eeeeeee....eeeeeeeeeee........eeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a4g A  76 EPEWTYPRLSCQGSTFQKALLISPHRFGEARGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHSYANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASKIGRWYSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 465
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465

Chain B from PDB  Type:PROTEIN  Length:390
 aligned with NRAM_INBBE | P27907 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:390
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465
           NRAM_INBBE    76 EPEWTYPRLSCQGSTFQKALLISPHRFGEARGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHSYANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASKIGRWYSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 465
               SCOP domains d1a4gb_ B: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1a4gB00 B:76-465  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeeeee.hhhh..........eeeeeeeee....eeeeeee.....................eeeeee..........eeeee..eeeeee....eeeeeee..hhh.eeeeee..eeeeeee.......ee.....eee..eeeeeeeee.....eeeeeeeee..eeeeee.........eeeeeee....eeeeeee........eeeeee....eeeeee...................................eeeee....eeeeeee.........eeeeeee...........eeeeeee........eeeeeee....eeeeeeeeeee........eeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a4g B  76 EPEWTYPRLSCQGSTFQKALLISPHRFGEARGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHSYANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASKIGRWYSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 465
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

1a	d1a4ga_	A:
1b	d1a4gb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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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 (strain b/beijing/1/87). Organism_taxid: 11525. Strain: b/beijing/1/87 (5)

1a	1a4gA00	A:76-465
1b	1a4gB00	B:76-465

(no "Pfam Domain" information available for 1A4G)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NRAM_INBBE | P27907)

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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	Cis Peptide Bonds
		Gln A:137 - Pro A:138	[ RasMol ]
		Gln B:137 - Pro B:138	[ RasMol ]
		Thr A:324 - Pro A:325	[ RasMol ]
		Thr B:324 - Pro B:325	[ RasMol ]

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	1a4g
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	NRAM_INBBE \| P27907	:	1a4q 1nsb 1nsc 1nsd

(no "Related Entries Specified in the PDB File" available for 1A4G)

Description

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Ligands, Modified Residues, Ions (3, 7)

Sites (13, 13)

SS Bonds (16, 16)

Cis Peptide Bonds (4, 4)

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