2YP9 - JenaLib

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:38 , THR A:318 , LEU A:381	BINDING SITE FOR MONO-SACCHARIDE NAG A1038 BOUND TO ASN A 38
2	AC2	SOFTWARE	GLU A:62 , ASN A:63 , TYR A:94 , HOH A:4109 , HOH A:4138	BINDING SITE FOR MONO-SACCHARIDE NAG A1063 BOUND TO ASN A 63
3	AC3	SOFTWARE	ASN A:126 , THR A:128 , HOH A:4237	BINDING SITE FOR MONO-SACCHARIDE NAG A1126 BOUND TO ASN A 126
4	AC4	SOFTWARE	ASN A:133 , HOH A:4194	BINDING SITE FOR MONO-SACCHARIDE NAG A1133 BOUND TO ASN A 133
5	AC5	SOFTWARE	SER A:45 , ASP A:77 , GLN A:80 , ASN A:81 , SER A:95 , PRO A:99 , TYR A:100 , GLU A:119 , PHE A:120 , ASN A:121 , ASN A:122 , GLY A:134 , THR A:135 , SER A:136 , SER A:137 , ARG A:141 , SER A:146 , PHE A:147 , PHE A:148 , SER A:149 , LEU A:151 , ALA A:163 , LEU A:164 , ASN A:165 , ASP A:190 , PHE A:193 , LEU A:194 , SER A:219 , PRO A:221 , ARG A:222 , ARG A:224 , ILE A:242 , ASN A:246 , SER A:247 , THR A:248 , ARG A:255 , GLU A:280 , ASN A:285 , VAL A:297 , GLU A:390 , GLU A:401 , GLU A:426 , HOH A:4116 , HOH A:4120 , HOH A:4141 , HOH A:4147 , HOH A:4196 , HOH A:4198 , HOH A:4199 , HOH A:4238 , HOH A:4261 , HOH A:4269 , HOH A:4291 , HOH A:4295 , HOH A:4298 , HOH A:4346 , HOH A:4359 , HOH A:4444 , HOH A:4578 , HOH A:4579 , HOH A:4580	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 165 RESIDUES 1165 TO 3165
6	AC6	SOFTWARE	SER A:45 , ASP A:77 , GLN A:80 , ASN A:81 , SER A:95 , PRO A:99 , TYR A:100 , GLU A:119 , PHE A:120 , ASN A:121 , ASN A:122 , GLY A:134 , THR A:135 , SER A:136 , SER A:137 , ARG A:141 , SER A:146 , PHE A:147 , PHE A:148 , SER A:149 , LEU A:151 , ALA A:163 , LEU A:164 , ASN A:165 , ASP A:190 , PHE A:193 , LEU A:194 , PRO A:221 , ARG A:222 , ARG A:224 , ILE A:242 , ASN A:246 , SER A:247 , THR A:248 , ARG A:255 , GLU A:280 , ASN A:285 , VAL A:297 , GLU A:390 , GLU A:401 , GLU A:426 , NAG A:1165 , MAN A:3165 , HOH A:4116 , HOH A:4120 , HOH A:4141 , HOH A:4147 , HOH A:4196 , HOH A:4198 , HOH A:4199 , HOH A:4261 , HOH A:4269 , HOH A:4291 , HOH A:4295 , HOH A:4346 , HOH A:4359 , HOH A:4444 , HOH A:4578 , HOH A:4579 , HOH A:4580	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 246 RESIDUES 1246 TO 2246
7	AC7	SOFTWARE	SER A:45 , ASN A:285 , VAL A:297 , HOH A:4346 , HOH A:4359	BINDING SITE FOR MONO-SACCHARIDE NAG A1285 BOUND TO ASN A 285

SS Bonds (6, 6)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:490
 aligned with I2D7A8_9INFA | I2D7A8 from UniProtKB/TrEMBL  Length:566

    Alignment length:496
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513      
         I2D7A8_9INFA    24 NSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACKRKSNNSFFSRLNWLTHLKFKYPALNVTMPNNEKFDKLYIWGVHHPGTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGIGQAADLKSTQAAINQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIK 519
               SCOP domains d2yp9a1 A:8-327 automated matches                                                                                                                                                                                                                                                                                               -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......eee.......eee..eee.ee......eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......ee....eeeeee..eee....eee.ee.......eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeee......eeee....eeeee..eee..eee.....ee......eeee.ee......eee..........------.................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yp9 A   8 NSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGGICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACKRKSNNSFFSRLNWLTHLKFKYPALNVTMPNNEKFDKLYIWGVHHPGTDNDQIFLYAQASGRITVSTKRSQQTVIPNIGSRPRVRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQ------AIAGFIENGWEGMVDGWYGFRHQNSEGIGQAADLKSTQAAINQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIK 503
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327      |337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497      
                                                                                                                                                                                                                                                                                                                                                         327    334

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

Asymmetric Unit(hide GO term definitions)

Chain A (I2D7A8_9INFA | I2D7A8)

molecular function
	GO:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0019065	receptor-mediated endocytosis of virus by host cell	Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
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:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

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		Ser A:54 - Pro A:55	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 16)

Sites (7, 7)