2J0O - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   SHIGELLA FLEXNERI IPAD

Authors :   S. Johnson, P. Roversi, S. M. Lea

Date :   04 Aug 06 (Deposition) - 02 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Shigella Flexneri, Type Iii Secretion, Cell Invasion, Ipad, T3Ss, Plasmid, Invasin, Virulence (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 Tip Proteins Ipad And Bipd.
J. Biol. Chem. V. 282 4035 2007
PubMed-ID: 17077085 | Reference-DOI: 10.1074/JBC.M607945200
(for further references see the PDB file header)

Molecule 1 - INVASIN IPAD
	Atcc	:	700930
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	DE3
	Fragment	:	RESIDUES 15-332
	Organism Scientific	:	SHIGELLA FLEXNERI
	Organism Taxid	:	623
	Strain	:	301
	Synonym	:	IPAD, 36 KDA MEMBRANE ANTIGEN
	Variant	:	SEROTYPE 2A

		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 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:286 , THR A:289 , GLU B:120	BINDING SITE FOR RESIDUE GOL A1323

(no "SS Bond" information available for 2J0O)

Asymmetric Unit

No.	Residues
1	Asn A:183	-	Asp A:184
2	Tyr A:212	-	Pro A:213
3	Asn A:266	-	Gly A:267
4	Gly B:182	-	Asn B:183
5	Asn B:183	-	Asp B:184
6	Gly B:185	-	Asn B:186
7	Tyr B:212	-	Pro B:213
8	Asn B:266	-	Gly B:267

Asymmetric Unit (9, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_IPAD_SHIFL_001 *	E	64	D	IPAD_SHIFL	---	---	A/B	E	64	D
2	UniProt	VAR_IPAD_SHIFL_002 *	N	102	H	IPAD_SHIFL	---	---	A/B	H	102	H
3	UniProt	VAR_IPAD_SHIFL_003 *	A	136	D	IPAD_SHIFL	---	---	A/B	A	136	D
4	UniProt	VAR_IPAD_SHIFL_004 *	N	140	K	IPAD_SHIFL	---	---	A/B	N	140	K
5	UniProt	VAR_IPAD_SHIFL_005 *	D	144	N	IPAD_SHIFL	---	---	A/B	D	144	N
6	UniProt	VAR_IPAD_SHIFL_006 *	N	193	K	IPAD_SHIFL	---	---	A/B	N	193	K
7	UniProt	VAR_IPAD_SHIFL_007 *	Q	220	K	IPAD_SHIFL	---	---	A/B	Q	220	K
8	UniProt	VAR_IPAD_SHIFL_008 *	Q	239	E	IPAD_SHIFL	---	---	A/B	Q	239	E
9	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)

Biological Unit 1 (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_IPAD_SHIFL_001 *	E	64	D	IPAD_SHIFL	---	---	A	E	64	D
2	UniProt	VAR_IPAD_SHIFL_002 *	N	102	H	IPAD_SHIFL	---	---	A	H	102	H
3	UniProt	VAR_IPAD_SHIFL_003 *	A	136	D	IPAD_SHIFL	---	---	A	A	136	D
4	UniProt	VAR_IPAD_SHIFL_004 *	N	140	K	IPAD_SHIFL	---	---	A	N	140	K
5	UniProt	VAR_IPAD_SHIFL_005 *	D	144	N	IPAD_SHIFL	---	---	A	D	144	N
6	UniProt	VAR_IPAD_SHIFL_006 *	N	193	K	IPAD_SHIFL	---	---	A	N	193	K
7	UniProt	VAR_IPAD_SHIFL_007 *	Q	220	K	IPAD_SHIFL	---	---	A	Q	220	K
8	UniProt	VAR_IPAD_SHIFL_008 *	Q	239	E	IPAD_SHIFL	---	---	A	Q	239	E
9	UniProt	VAR_IPAD_SHIFL_009 *	S	247	N	IPAD_SHIFL	---	---	A	S	247	N
	* ID not provided by source

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

Biological Unit 2 (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_IPAD_SHIFL_001 *	E	64	D	IPAD_SHIFL	---	---	B	E	64	D
2	UniProt	VAR_IPAD_SHIFL_002 *	N	102	H	IPAD_SHIFL	---	---	B	H	102	H
3	UniProt	VAR_IPAD_SHIFL_003 *	A	136	D	IPAD_SHIFL	---	---	B	A	136	D
4	UniProt	VAR_IPAD_SHIFL_004 *	N	140	K	IPAD_SHIFL	---	---	B	N	140	K
5	UniProt	VAR_IPAD_SHIFL_005 *	D	144	N	IPAD_SHIFL	---	---	B	D	144	N
6	UniProt	VAR_IPAD_SHIFL_006 *	N	193	K	IPAD_SHIFL	---	---	B	N	193	K
7	UniProt	VAR_IPAD_SHIFL_007 *	Q	220	K	IPAD_SHIFL	---	---	B	Q	220	K
8	UniProt	VAR_IPAD_SHIFL_008 *	Q	239	E	IPAD_SHIFL	---	---	B	Q	239	E
9	UniProt	VAR_IPAD_SHIFL_009 *	S	247	N	IPAD_SHIFL	---	---	B	S	247	N
	* ID not provided by source

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

(no "PROSITE Motif" information available for 2J0O)

(no "Exon" information available for 2J0O)

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:284
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:284
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318    
           IPAD_SHIFL    39 HPVSSLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRNEYPINKDARELLHSAPKEAELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSC 322
               SCOP domains d2j0oa1 A:39-322 Invasin IpaD                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeehhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeeee....eeeee.hhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------D-------------------------------------H---------------------------------D---K---N------------------------------------------------K--------------------------K------------------E-------N--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j0o A  39 HPVSSLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRHEYPINKDARELLHSAPKEAELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSC 322
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:284
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318    
           IPAD_SHIFL    39 HPVSSLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRNEYPINKDARELLHSAPKEAELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSC 322
               SCOP domains d2j0ob_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......eeehhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeeee....eeeee.hhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------D-------------------------------------H---------------------------------D---K---N------------------------------------------------K--------------------------K------------------E-------N--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j0o B  39 HPVSSLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRHEYPINKDARELLHSAPKEAELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSC 322
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

d2j0ob_

Protein domain: Invasin IpaD (3)

Shigella flexneri [TaxId: 623] (3)

d2j0oa1

A:39-322

(no "CATH Domain" information available for 2J0O)

(no "Pfam Domain" information available for 2J0O)

Asymmetric 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 Unit
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	Sites
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	Cis Peptide Bonds
		Asn A:183 - Asp A:184	[ RasMol ]
		Asn A:266 - Gly A:267	[ RasMol ]
		Asn B:183 - Asp B:184	[ RasMol ]
		Asn B:266 - Gly B:267	[ RasMol ]
		Gly B:182 - Asn B:183	[ RasMol ]
		Gly B:185 - Asn B:186	[ RasMol ]
		Tyr A:212 - Pro A:213	[ RasMol ]
		Tyr B:212 - Pro B:213	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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

2j0n	A PROTEOLYTICALLY TRUNCATED FORM OF SHIGELLA FLEXNERI IPAD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 18)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

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