1DYQ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STAPHYLOCOCCAL ENTEROTOXIN A MUTANT VACCINE

Authors :   H. I. Krupka, B. W. Segelke, B. Rupp

Date :   05 Feb 00 (Deposition) - 19 Mar 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Enterotoxin, Staphylococcal Enterotoxin Type A, Vaccine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. I. Krupka, B. W. Segelke, R. Ulrich, S. Ringhofer, M. Knapp, B. Rupp
Structural Basis For Abrogated Binding Between Staphylococcal Enterotoxin A Superantigen Vaccine And Mhc-Ii?
Protein Sci. V. 11 642 2002
PubMed-ID: 11847286 | Reference-DOI: 10.1110/PS.39702

Molecule 1 - STAPHYLOCOCCAL ENTEROTOXIN A MUTANT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	FDA196E
	Expression System Plasmid	:	PSE380
	Expression System Strain	:	JM101
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Other Details	:	MUTANT GENE
	Strain	:	A
	Synonym	:	SEA

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:44 , HIS A:187 , HIS A:225 , ASP A:227	BINDING SITE FOR RESIDUE ZN A 234
2	AC2	SOFTWARE	TYR A:64 , GLY A:93 , TYR A:94 , ARG A:211 , ARG A:214 , HOH A:2490 , HOH A:2491 , HOH A:2492 , HOH A:2493 , HOH A:2494	BINDING SITE FOR RESIDUE SO4 A 235

Asymmetric/Biological Unit

No.	Residues
1	A:96	-	A:106

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

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	STAPH_STREP_TOXIN_1	PS00277	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1.	ETXA_STAAU	132-141	1	A:108-117
1	STAPH_STREP_TOXIN_1	PS00277		ETXA_STAAW	132-141	1	A:108-117
2	STAPH_STREP_TOXIN_2	PS00278	Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.	ETXA_STAAU	171-194	1	A:147-170
2	STAPH_STREP_TOXIN_2	PS00278		ETXA_STAAW	171-194	1	A:147-170

(no "Exon" information available for 1DYQ)

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:228
 aligned with ETXA_STAAU | P0A0L2 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:228
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249        
           ETXA_STAAU    30 EINEKDLRKKSELQGTALGNLKQIYYYNEKAKTENKESHDQFLQHTILFKGFFTDHSWYNDLLVDFDSKDIVDKYKGKKVDLYGAYYGYQCAGGTPNKTACMYGGVTLHDNNRLTEEKKVPINLWLDGKQNTVPLETVKTNKKNVTVQELDLQARRYLQEKYNLYNSDVFDGKVQRGLIVFHTSTEPSVNYDLFGAQGQYSNTLLRIYRDNKTINSENMHIDIYLYTS 257
               SCOP domains d1dyqa1 A:6-120 Staphylococcal enterotoxin A, SEA                                                                  d1dyqa2 A:121-233 Staphylococcal enterotoxin A, SEA                                                               SCOP domains
               CATH domains 1dyqA02 A:6-31,A:117-232  1dyqA01 A:32-114  [code=2.40.50.110, no name defined]                              --1dyqA02 A:6-31,A:117-232  [code=3.10.20.120, no name defined]                                                       - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.hhhhh..hhhhhhhhhhhh..eeeeeee.........eeee...........eeeee..hhhhhhhhh...eeeeeeeehhhh.......eeeee..eee....eeeeeee..eeeee..eee.......eeee.eeehhhhhhhhhhhhhhhhh...hhhhh....eeeeeee......eeee.......hhhhhhhhhh...eee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------STAPH_STRE-----------------------------STAPH_STREP_TOXIN_2     --------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dyq A   6 EINEKDLRKKSELQGTALGNLKQIYYYNEKAKTENKESHDQFRQHTILFKGFFTDHSWYNDLLVRFDSKDIVDKYKGKKVDLYGAYAGYQCAGGTPNKTACMYGGVTLHDNNRLTEEKKVPINLWLDGKQNTVPLETVKTNKKNVTVQELDLQARRYLQEKYNLYNSDVFDGKVQRGLIVFHTSTEPSVNYDLFGAQGQYSNTLLRIYRDNKTINSENMHIDIYLYTS 233
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225

Chain A from PDB  Type:PROTEIN  Length:228
 aligned with ETXA_STAAW | P0A0L1 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:228
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249        
           ETXA_STAAW    30 EINEKDLRKKSELQGTALGNLKQIYYYNEKAKTENKESHDQFLQHTILFKGFFTDHSWYNDLLVDFDSKDIVDKYKGKKVDLYGAYYGYQCAGGTPNKTACMYGGVTLHDNNRLTEEKKVPINLWLDGKQNTVPLETVKTNKKNVTVQELDLQARRYLQEKYNLYNSDVFDGKVQRGLIVFHTSTEPSVNYDLFGAQGQYSNTLLRIYRDNKTINSENMHIDIYLYTS 257
               SCOP domains d1dyqa1 A:6-120 Staphylococcal enterotoxin A, SEA                                                                  d1dyqa2 A:121-233 Staphylococcal enterotoxin A, SEA                                                               SCOP domains
               CATH domains 1dyqA02 A:6-31,A:117-232  1dyqA01 A:32-114  [code=2.40.50.110, no name defined]                              --1dyqA02 A:6-31,A:117-232  [code=3.10.20.120, no name defined]                                                       - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.hhhhh..hhhhhhhhhhhh..eeeeeee.........eeee...........eeeee..hhhhhhhhh...eeeeeeeehhhh.......eeeee..eee....eeeeeee..eeeee..eee.......eeee.eeehhhhhhhhhhhhhhhhh...hhhhh....eeeeeee......eeee.......hhhhhhhhhh...eee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------STAPH_STRE-----------------------------STAPH_STREP_TOXIN_2     --------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dyq A   6 EINEKDLRKKSELQGTALGNLKQIYYYNEKAKTENKESHDQFRQHTILFKGFFTDHSWYNDLLVRFDSKDIVDKYKGKKVDLYGAYAGYQCAGGTPNKTACMYGGVTLHDNNRLTEEKKVPINLWLDGKQNTVPLETVKTNKKNVTVQELDLQARRYLQEKYNLYNSDVFDGKVQRGLIVFHTSTEPSVNYDLFGAQGQYSNTLLRIYRDNKTINSENMHIDIYLYTS 233
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225

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 "Pfam Domain" information available for 1DYQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ETXA_STAAU | P0A0L2)

molecular function
	GO:0042289	MHC class II protein binding	Interacting selectively and non-covalently with major histocompatibility complex class II molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A (ETXA_STAAW | P0A0L1)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dyq)

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	ETXA_STAAW \| P0A0L1
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UniProtKB/Swiss-Prot
	ETXA_STAAU \| P0A0L2	:	1esf 1i4g 1i4h 1lo5 1sea 1sxt 5fk9
	ETXA_STAAW \| P0A0L1	:	1sea

1esf	STAPHYLOCOCCAL ENTEROTOXIN A (STAPHYLOCOCCUS AUREUS)
1sea	STAPHYLOCOCCAL ENTEROTOXIN A (THEORETICAL MODEL)
1sxt	STAPHYLOCOCCAL ENTEROTOXIN TYPE A (SEA) CO-CRYSTALLISED WITH ZINC (STAPHYLOCOCCUS AUREUS)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (5, 8)

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