4ES8 - 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 :   CRYSTAL STRUCTURE OF THE ADHESIN DOMAIN OF EPF FROM STREPTOCOCCUS PYOGENES IN P212121

Authors :   C. Linke, N. Siemens, B. Kreikemeyer, E. N. Baker

Date :   23 Apr 12 (Deposition) - 19 Sep 12 (Release) - 19 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.58

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

Keywords :   Carbohydrate-Binding Module, Fibronectin-Like Domain, Adhesin, Extracellular, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Linke, N. Siemens, S. Oehmcke, M. Radjainia, R. H. Law, J. C. Whisstock, E. N. Baker, B. Kreikemeyer
The Extracellular Protein Factor Epf From Streptococcus Pyogenes Is A Cell Surface Adhesin That Binds To Cells Through An N-Terminal Domain Containing A Carbohydrate-Binding Module.
J. Biol. Chem. V. 287 38178 2012
PubMed-ID: 22977243 | Reference-DOI: 10.1074/JBC.M112.376434
(for further references see the PDB file header)

Molecule 1 - EPF
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PASK_IBA2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	SPYOM01000212
	Organism Scientific	:	STREPTOCOCCUS PYOGENES
	Organism Taxid	:	294934
	Strain	:	M49 591

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	K	1	Ligand/Ion	POTASSIUM ION
4	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:63 , ASN A:64 , PHE A:65 , LYS A:143 , HOH A:737 , HOH A:821 , LYS B:66 , ASP B:74	BINDING SITE FOR RESIDUE GOL A 501
2	AC2	SOFTWARE	ARG A:79 , LEU A:93 , ILE A:94 , VAL A:99 , HOH A:680	BINDING SITE FOR RESIDUE ACT A 502
3	AC3	SOFTWARE	TYR A:114 , ARG A:125 , LYS A:127 , HOH A:1043	BINDING SITE FOR RESIDUE ACT A 503
4	AC4	SOFTWARE	VAL A:194 , HOH A:743 , HOH A:957 , SER B:188 , HOH B:792 , HOH B:884	BINDING SITE FOR RESIDUE NA A 504
5	AC5	SOFTWARE	HOH A:640 , SER B:172 , ASN B:175 , ASP B:180 , SER B:181 , HOH B:615 , HOH B:629 , HOH B:723	BINDING SITE FOR RESIDUE K B 501

(no "SS Bond" information available for 4ES8)

Asymmetric Unit

No.	Residues
1	Ala A:132	-	Pro A:133
2	Asn A:308	-	Pro A:309
3	Ala B:132	-	Pro B:133
4	Asn B:308	-	Pro B:309

(no "SAP(SNP)/Variant" information available for 4ES8)

(no "PROSITE Motif" information available for 4ES8)

(no "Exon" information available for 4ES8)

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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.............eeeeee....eeee...hhhhh.....ee......eeeee...eeeeee.......eeeeeeeee.......eeeeeeeeeee...eeeeeeeee........eee..hhhhheeeeee............eeeeeeeee.....eeeeeeeee.......eeeeeeeeeeee.....eeeeee......eeeeeee..........eeeeee.....eeeeee........eeee.hhhhhhhh....eeeeeeee.........eeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4es8 A  56 EELPDDLMNFKGTWEVSADGSSGRFFSKGATDSYVFHLIPAKDVKKPGWREHNEVKDSYIKIDKQSIAARYKTSTTAPYSVAFKVNTKSLIKDHDYKITFEQGQIASGITVDYRIGSAFNKTTDDSFKISDESKYASNVKIEGEEQGFKQREQGDKTISFRTLKEGPMSLVLLSKVEKKPQGDLDVEFKNLKIIDVTNPSQLDKGVAYVGNKNVQLTLKSDDGRTNFEGDEISLFNSRGELLQTVTVTKDQQNPISITLSEDQAKSLKNKEKLKVSIKQKQSKKTSKDFFFEVGIDPKVEAK 357
                                    65        75        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

Chain B from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.............eeeeee....eeee...hhhhh.....ee......eeeee...eeeeee.......eeeeeeeee.......eeeeeeeeeee...eeeeeeeee........eee..hhhhheeeeee............eeeeeeeee.....eeeeeeeee.......eeeeeeeeeeee.....eeeeee......eeeeeee..........eeeeee.....eeeeee........eeee.hhhhhhhh....eeeeeeee.........eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4es8 B  57 ELPDDLMNFKGTWEVSADGSSGRFFSKGATDSYVFHLIPAKDVKKPGWREHNEVKDSYIKIDKQSIAARYKTSTTAPYSVAFKVNTKSLIKDHDYKITFEQGQIASGITVDYRIGSAFNKTTDDSFKISDESKYASNVKIEGEEQGFKQREQGDKTISFRTLKEGPMSLVLLSKVEKKPQGDLDVEFKNLKIIDVTNPSQLDKGVAYVGNKNVQLTLKSDDGRTNFEGDEISLFNSRGELLQTVTVTKDQQNPISITLSEDQAKSLKNKEKLKVSIKQKQSKKTSKDFFFEVGIDPK 353
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346

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 4ES8)

(no "CATH Domain" information available for 4ES8)

(no "Pfam Domain" information available for 4ES8)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4ES8)

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ 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 ]

	Cis Peptide Bonds
		Ala A:132 - Pro A:133	[ RasMol ]
		Ala B:132 - Pro B:133	[ RasMol ]
		Asn A:308 - Pro A:309	[ RasMol ]
		Asn B:308 - Pro B:309	[ RasMol ]

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
	4es8
		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
	A0A0H3BY62_S \| A0A0H3BY62
		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
	A0A0H3BY62_S \| A0A0H3BY62
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	A0A0H3BY62_S \| A0A0H3BY62	:	4es9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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