4DXG - JenaLib

Title :   CRYSTAL STRUCTURE OF STAPHYLOCOCCAL SUPERANTIGEN-LIKE PROTEIN 4 COMPLEXED WITH SIALYL LEWIS X

Authors :   S. J. Hermans, H. M. Baker, R. J. Langley, E. N. Baker, J. F. Fraser

Date :   27 Feb 12 (Deposition) - 19 Sep 12 (Release) - 12 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Oligonucleotide/Oligosaccharide Binding Fold, Beta Grasp Fold, Superantigen Fold, Carbohydrate Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Hermans, H. M. Baker, R. P. Sequeira, R. J. Langley, E. N. Baker, J. D. Fraser
Structural And Functional Properties Of Staphylococcal Superantigen-Like Protein 4
Infect. Immun. V. 80 4004 2012
PubMed-ID: 22949551 | Reference-DOI: 10.1128/IAI.00764-12

Compounds

Molecule 1 - STAPHYLOCOCCAL ENTEROTOXIN-LIKE TOXIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-32A.3C
	Expression System Strain	:	AD494
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 109-308
	Gene	:	NWMN_0391, SSL4NM
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	426430
	Strain	:	NEWMAN
	Synonym	:	SUPERANTIGEN-LIKE PROTEIN 4

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 7)

Asymmetric/Biological Unit (6, 7)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5	PIN	1	Ligand/Ion	PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
6	SIA	1	Ligand/Ion	O-SIALIC ACID

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:22 , ASP A:48 , TYR A:49 , PHE A:50 , LEU A:78 , ASN A:97 , LYS A:99 , LYS A:100 , VAL A:101 , LYS A:126 , THR A:128 , HOH A:437 , HOH A:452 , HOH A:460	BINDING SITE FOR RESIDUE PIN A 305
2	AC2	SOFTWARE	LYS A:21 , GLU A:80	BINDING SITE FOR RESIDUE CL A 306
3	AC3	SOFTWARE	ASP A:102 , HIS A:103 , LYS A:104 , GLU A:124 , LEU A:134 , LYS A:169 , TYR A:170 , THR A:171 , GLU A:173 , LYS A:176 , GLN A:179 , ASN A:181 , ARG A:182 , ASP A:185 , ILE A:192 , ASP A:193 , HOH A:410 , HOH A:435	BINDING SITE FOR LINKED RESIDUES A 301 to 304

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:194
 aligned with A0A0H3K6A3_S | A0A0H3K6A3 from UniProtKB/TrEMBL  Length:308

    Alignment length:194
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    
         A0A0H3K6A3_S   115 EINPKFKDLRAYYTKPSLEFKNEIGIILKKWTTIRFMNVVPDYFIYKIALVGKDDKKYGEGVHRNVDVFVVLEENNYNLEKYSVGGITKSNSKKVDHKAGVRITKEDNKGTISHDVSEFKITKEQISLKELDFKLRKQLIEKNNLYGNVGSGKIVIKMKNGGKYTFELHKKLQENRMADVIDGTNIDNIEVNIK 308
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....eeeeeeeeee........eeee......eeee...hhhhhh..eeeeeeeeee...........eee..eee.......eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhhh.......eeeeeee....eeeee.....hhhhhh.eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxg A   7 EINPKFKDLRAYYTKPSLEFKNEIGIILKKWTTIRFMNVVPDYFIYKIALVGKDDKKYGEGVHRNVDVFVVLEENNYNLEKYSVGGITKSNSKKVDHKAGVRITKEDNKGTISHDVSEFKITKEQISLKELDFKLRKQLIEKNNLYGNVGSGKIVIKMKNGGKYTFELHKKLQENRMADVIDGTNIDNIEVNIK 200
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Asymmetric/Biological 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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PIN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SIA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

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

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4dxg
		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
	A0A0H3K6A3_S \| A0A0H3K6A3
		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

Analysis Tools

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
	A0A0H3K6A3_S \| A0A0H3K6A3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description