2JAA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   SEMET SUBSTITUTED SHIGELLA FLEXNERI IPAD

Authors :   S. Johnson, P. Roversi, M. Espina, A. Olive, J. E. Deane, S. Birket, T. Fi W. D. Picking, A. J. Blocker, E. E. Galyov, W. L. Picking, S. M. Lea

Date :   24 Nov 06 (Deposition) - 30 Nov 06 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ipad, T3Ss, Semet, Invasin, Virulence, Cell Invasion, Shigella Flexneri, Type Iii Secretion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Johnson, P. Roversi, M. Espina, A. Olive, J. E. Deane, S. Birket, T. Field, W. D. Picking, A. J. Blocker, E. E. Galyov, W. L. Picking, S. M. Lea
Self-Chaperoning Of The Type Iii Secretion System Needle Ti Proteins Ipad And Bipd.
J. Biol. Chem. V. 282 4035 2007
PubMed-ID: 17077085 | Reference-DOI: 10.1074/JBC.M607945200

Molecule 1 - INVASIN IPAD
	Atcc	:	700930
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 121-332
	Organism Scientific	:	SHIGELLA FLEXNERI
	Organism Taxid	:	623
	Other Details	:	PROTELYSIS PRODUCT. SEMET SUBSTITUTED
	Strain	:	301
	Variant	:	SEROTYPE 2A

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2JAA)

(no "SS Bond" information available for 2JAA)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:212	-	Pro A:213
2	Ile A:319	-	Ser A:320
3	Asp B:124	-	Gly B:125
4	Tyr B:212	-	Pro B:213
5	Ile B:319	-	Ser B:320

Asymmetric/Biological Unit (7, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_IPAD_SHIFL_003 *	A	136	D	IPAD_SHIFL	---	---	A/B	A	136	D
2	UniProt	VAR_IPAD_SHIFL_004 *	N	140	K	IPAD_SHIFL	---	---	A/B	N	140	K
3	UniProt	VAR_IPAD_SHIFL_005 *	D	144	N	IPAD_SHIFL	---	---	A/B	D	144	N
4	UniProt	VAR_IPAD_SHIFL_006 *	N	193	K	IPAD_SHIFL	---	---	A/B	N	193	K
5	UniProt	VAR_IPAD_SHIFL_007 *	Q	220	K	IPAD_SHIFL	---	---	A/B	Q	220	K
6	UniProt	VAR_IPAD_SHIFL_008 *	Q	239	E	IPAD_SHIFL	---	---	A/B	Q	239	E
7	UniProt	VAR_IPAD_SHIFL_009 *	S	247	N	IPAD_SHIFL	---	---	A/B	S	247	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2JAA)

(no "Exon" information available for 2JAA)

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:167
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:193
                                   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317   
           IPAD_SHIFL   128 MISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTIS 320
               SCOP domains d2jaaa1 A:128-320 Invasin IpaD                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...--------------.hhhhhhhhhhhhhh...eee........hhhhhhhhhhh...eeeeee..eeeeee.hhhhhhhhh..------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------D---K---N------------------------------------------------K--------------------------K------------------E-------N------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jaa A 128 mISHRELWAKIANSINDINEQYLKVYEHAVSSYTQmYQDFSAVLSSLAGW--------------VNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINmTPIDNmLKSL------------NAKYQAWNAGFSAEDETmKNNLQTLVQKYSNANSIFDNLVKVLSSTIS 320
                            |      137       147       157     | 167       177         -    |  197       207       217       227       237       247  |    257  |      -     | 277       287  |    297       307       317   
                            |                                163-MSE       177            192                                                       250-MSE | 260          273              290-MSE                          
                          128-MSE                                                                                                                         256-MSE

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:198
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312        
           IPAD_SHIFL   123 LDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTIS 320
               SCOP domains d2jaab_ B: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.-------.eehhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhh...eeeeee..eeeeee.hhhhhhhhhhh...---------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------D---K---N------------------------------------------------K--------------------------K------------------E-------N------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jaa B 123 LDGDQmISHRELWAKIANSINDINEQYLKVYEHAVSSYTQmYQDFSAVLSSLAGWISP-------VKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINmTPIDNmLKSLDNL---------NAKYQAWNAGFSAEDETmKNNLQTLVQKYSNANSIFDNLVKVLSSTIS 320
                                 | 132       142       152       162|      172       | -     | 192       202       212       222       232       242       252   |   262|        -|      282       292       302       312        
                               128-MSE                            163-MSE          180     188                                                           250-MSE |    263       273              290-MSE                          
                                                                                                                                                               256-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: IpaD-like (12)

Superfamily: IpaD-like (12)

Family: IpaD-like (10)

Protein domain: automated matches (3)

Shigella flexneri [TaxId: 623] (3)

d2jaab_

Protein domain: Invasin IpaD (3)

Shigella flexneri [TaxId: 623] (3)

d2jaaa1

A:128-320

(no "CATH Domain" information available for 2JAA)

(no "Pfam Domain" information available for 2JAA)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IPAD_SHIFL | P18013)

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
	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
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 2jaa)

	Cis Peptide Bonds
		Asp B:124 - Gly B:125	[ RasMol ]
		Ile A:319 - Ser A:320	[ RasMol ]
		Ile B:319 - Ser B:320	[ RasMol ]
		Tyr A:212 - Pro A:213	[ RasMol ]
		Tyr B:212 - Pro B:213	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit 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
	2jaa
		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
	IPAD_SHIFL \| P18013
		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)
	(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
	IPAD_SHIFL \| P18013
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	IPAD_SHIFL \| P18013	:	2j0n 2j0o 3r9v 4d3e

2j0n	A PROTEOLYTICALLY TRUNCATED FORM OF SHIGELLA FLEXNERI IPAD
2j0o	SHIGELLA FLEXNERI IPAD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 10)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 14)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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