4YYB - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE STRUCTURE OF HEMAGGLUTININ FROM A H6N1 INFLUENZA VIRUS (A/TAIWAN/2/2013) IN COMPLEX WITH HUMAN RECEPTOR ANALOG 6'SLNLN

Authors :   F. Wang, J. Qi, Y. Bi, W. Zhang, M. Wang, M. Wang, J. Liu, J. Yan, Y. Shi, G. F

Date :   23 Mar 15 (Deposition) - 13 Apr 16 (Release) - 13 Apr 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.61

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Hemagglutinin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Wang, J. Qi, Y. Bi, W. Zhang, M. Wang, M. Wang, J. Liu, J. Yan, Y. Shi, G. F. Gao
Structure Of Hemagglutinin From A H6N1 Influenza Virus (A/Taiwan/2/2013) At 2. 6 Angstroms Resolution
To Be Published
PubMed: search

Molecule 1 - HA1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	INSECT CELL EXPRESSION VECTOR PTIE1
	Expression System Taxid	:	266783
	Organism Scientific	:	UNIDENTIFIED INFLUENZA VIRUS
	Organism Taxid	:	119212

Molecule 2 - HA2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	INSECT CELL EXPRESSION VECTOR PTIE1
	Expression System Taxid	:	266783
	Organism Scientific	:	UNIDENTIFIED INFLUENZA VIRUS
	Organism Taxid	:	119212

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SIA	1	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (4, 21)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SIA	3	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:138 , GLU B:476 , HOH B:602	binding site for Poly-Saccharide residues NAG B 501 through BMA B 503 bound to ASN B 483
2	AC2	SOFTWARE	TYR A:91 , ARG A:129 , VAL A:131 , THR A:132 , ASN A:133 , GLY A:223 , GLN A:224 , SER A:226	binding site for Poly-Saccharide residues SIA A 603 through GAL A 604

Asymmetric Unit

No.	Residues
1	A:4	-	B:466
2	A:42	-	A:277
3	A:55	-	A:67
4	A:90	-	A:135
5	A:281	-	A:305
6	B:473	-	B:477

(no "Cis Peptide Bond" information available for 4YYB)

(no "SAP(SNP)/Variant" information available for 4YYB)

(no "PROSITE Motif" information available for 4YYB)

(no "Exon" information available for 4YYB)

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:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhh.....ee...eee...........eee.hhhhhhhhhhheeeeeeee..hhhhh.........................eee...........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee......eee....eeeeee.eee..ee......ee.....eee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yyb A   1 DKICIGYHANNSTTQVDTLLEKNVTVTHSVELLENQKEKRFCKIMNKAPLDLKDCTIEGWILGNPKCDLLLGDQSWSYIVERPNAQNGICYPGVLNELEELKAFIGSGERVERFEMFPKSTWAGVDTSRGVTNACPSYTLDSSFYRNLVWLVKTDSATYPVIKGTYNNTGTQPILYFWGVHHPLDTTVQDNLYGSGDKYVRMGTESMNFAKSPEIAARPAVNGQRSRIDYYWSVLRPGETLNVESNGNLIAPWYAYKFVSTNKKGAVFKSDLPIENCDATCQTITGVLRTNKTFQNVSPLWIGECPKYVKSESLRLATGLRNVPQ 325
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yyb B 330 GIFGAIAGFIEGGWTGMIDGWYGYHHENSQGSGYAADRESTQKAIDGITNKVNSIINKMNTQFEAVDHEFSNLERRIGNLNKRMEDGFLDVWTYNAELLVLLENERTLDLHDANVKNLYEKVKSQLRDNANDLGNGCFEFWHKCDNECMESVKNGTYDYPKY 491
                                   339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489

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 '\|'

(no "SCOP Domain" information available for 4YYB)

(no "CATH Domain" information available for 4YYB)

(no "Pfam Domain" information available for 4YYB)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4YYB)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SIA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4yyb)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4yyb
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	A0A0J9X267_9 \| A0A0J9X267
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	A0A0J9X268_9 \| A0A0J9X268
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	A0A0J9X267_9 \| A0A0J9X267
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	A0A0J9X268_9 \| A0A0J9X268
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (2, 2)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File