1Z4X - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PARAINFLUENZA VIRUS 5 (SV5) HEMAGGLUTININ-NEURAMINIDASE (HN) WITH LIGAND SIALYLLACTOSE (SOAKED WITH SIALYLLACTOSE, PH8.0)

Authors :   P. Yuan, T. B. Thompson, B. A. Wurzburg, R. G. Paterson, R. A. Lamb, T. S. J

Date :   16 Mar 05 (Deposition) - 24 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)
Biol. Unit 2: A  (2x)

Keywords :   Hemagglutinin, Neuraminidase, Fusion, Tetramer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Yuan, T. B. Thompson, B. A. Wurzburg, R. G. Paterson, R. A. Lamb, T. S. Jardetzky
Structural Studies Of The Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Tetramer In Complex With Its Receptor, Sialyllactose.
Structure V. 13 803 2005
PubMed-ID: 15893670 | Reference-DOI: 10.1016/J.STR.2005.02.019

Molecule 1 - HEMAGGLUTININ-NEURAMINIDASE
	Chains	:	A
	EC Number	:	3.2.1.18
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Plasmid	:	PBACGUS-3
	Expression System Taxid	:	7111
	Expression System Vector Type	:	VIRUS
	Fragment	:	EXTRACELLULAR DOMAIN
	Gene	:	HN
	Organism Scientific	:	SIMIAN VIRUS 5
	Organism Taxid	:	11207
	Strain	:	W3

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	SLT	1	Ligand/Ion	5-(ACETYLAMINO)-3,5-DIDEOXYNON-2-ULOPYRANONOSYL-(2->3)-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)HEXOPYRANOSE

Biological Unit 1 (3, 24)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	16	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	4	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	SLT	4	Ligand/Ion	5-(ACETYLAMINO)-3,5-DIDEOXYNON-2-ULOPYRANONOSYL-(2->3)-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)HEXOPYRANOSE

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	SLT	2	Ligand/Ion	5-(ACETYLAMINO)-3,5-DIDEOXYNON-2-ULOPYRANONOSYL-(2->3)-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)HEXOPYRANOSE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:139	BINDING SITE FOR RESIDUE NDG A 1
2	AC2	SOFTWARE	NAG A:3 , ASN A:267 , THR A:269 , GLN A:369	BINDING SITE FOR RESIDUE NAG A 2
3	AC3	SOFTWARE	NAG A:2 , GLN A:369	BINDING SITE FOR RESIDUE NAG A 3
4	AC4	SOFTWARE	NAG A:5 , GLU A:481 , ASN A:504 , THR A:506 , GLN A:507 , ILE A:509 , HOH A:1120	BINDING SITE FOR RESIDUE NAG A 4
5	AC5	SOFTWARE	NAG A:4 , GLN A:507 , HOH A:1046	BINDING SITE FOR RESIDUE NAG A 5
6	AC6	SOFTWARE	ASP A:250 , SER A:253 , ALA A:255 , ALA A:285	BINDING SITE FOR RESIDUE CA A 601
7	AC7	SOFTWARE	ARG A:163 , GLU A:247 , ASN A:288 , TYR A:306 , GLU A:390 , ARG A:405 , ASN A:407 , ARG A:495 , TYR A:523 , HOH A:960 , HOH A:1026 , HOH A:1044 , HOH A:1084 , HOH A:1141 , HOH A:1161	BINDING SITE FOR RESIDUE SLT A 923

Asymmetric Unit

No.	Residues
1	A:161	-	A:185
2	A:175	-	A:236
3	A:227	-	A:240
4	A:365	-	A:375
5	A:448	-	A:458
6	A:528	-	A:539

(no "Cis Peptide Bond" information available for 1Z4X)

(no "SAP(SNP)/Variant" information available for 1Z4X)

(no "PROSITE Motif" information available for 1Z4X)

(no "Exon" information available for 1Z4X)

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:448
 aligned with HN_PIV5 | P04850 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:448
                                   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       507       517       527       537       547       557        
              HN_PIV5   118 INDNRYINGINQFYFSIAEGRNLTLGPLLNMPSFIPTATTPEGCTRIPSFSLTKTHWCYTHNVILNGCQDHVSSNQFVSMGIIEPTSAGFPFFRTLKTLYLSDGVNRKSCSISTVPGGCMMYCFVSTQPERDDYFSAAPPEQRIIIMYYNDTIVERIINPPGVLDVWATLNPGTGSGVYYLGWVLFPIYGGVIKGTSLWNNQANKYFIPQMVAALCSQNQATQVQNAKSSYYSSWFGNRMIQSGILACPLRQDLTNECLVLPFSNDQVLMGAEGRLYMYGDSVYYYQRSNSWWPMTMLYKVTITFTNGQPSAISAQNVPTQQVPRPGTGDCSATNRCPGFCLTGVYADAWLLTNPSSTSTFGSEATFTGSYLNTATQRINPTMYIANNTQIISSQQFGSSGQEAAYGHTTCFRDTGSVMVYCIYIIELSSSLLGQFQIVPFIRQVTLS 565
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhh.eeeeee...............eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee..eeeeeeee...hhhhhhhh....eeeeeeee....eeeeee........eeeeee.....eee..eeeeeeeeee...hhhhhhhh...............hhhhhhhhhhhh.ee.....eeeeeeeeeee.........eeee...........eeeeee..eeeeee.........eeeeeeeee....eeeeeeee..........hhhhh................eee..hhhhh........eeeeee........eeeeee....eeeeee.......eeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z4x A 118 INDNRYINGINQFYFSIAEGRNLTLGPLLNMPSFIPTATTPEGCTRIPSFSLTKTHWCYTHNVILNGCQDHVSSNQFVSMGIIEPTSAGFPFFRTLKTLYLSDGVNRKSCSISTVPGGCMMYCFVSTQPERDDYFSAAPPEQRIIIMYYNDTIVERIINPPGVLDVWATLNPGTGSGVYYLGWVLFPIYGGVIKGTSLWNNQANKYFIPQMVAALCSQNQATQVQNAKSSYYSSWFGNRMIQSGILACPLRQDLTNECLVLPFSNDQVLMGAEGRLYMYGDSVYYYQRSNSWWPMTMLYKVTITFTNGQPSAISAQNVPTQQVPRPGTGDCSATNRCPGFCLTGVYADAWLLTNPSSTSTFGSEATFTGSYLNTATQRINPTMYIANNTQIISSQQFGSSGQEAAYGHTTCFRDTGSVMVYCIYIIELSSSLLGQFQIVPFIRQVTLS 565
                                   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       507       517       527       537       547       557

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 1Z4X)

(no "CATH Domain" information available for 1Z4X)

(no "Pfam Domain" information available for 1Z4X)

Asymmetric Unit(hide GO term definitions)

Chain A (HN_PIV5 | P04850)

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:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
	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.
biological process
	GO:0046761	viral budding from plasma membrane	A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
	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:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	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.

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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SLT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1z4x)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 \| Biol. Unit 2 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
	1z4x
		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
	HN_PIV5 \| P04850
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.1.18
		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
	HN_PIV5 \| P04850
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HN_PIV5 \| P04850	:	1z4v 1z4w 1z4y 1z4z 1z50 3tsi 4jf7

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

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 (18, 18)

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