3R9V - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   COCRYSTAL STRUCTURE OF PROTEOLYTICALLY TRUNCATED FORM OF IPAD FROM SHIGELLA FLEXNERI BOUND TO DEOXYCHOLATE

Authors :   M. L. Barta, N. E. Dickenson, W. L. Picking, W. D. Picking, B. V. Geisbrec

Date :   26 Mar 11 (Deposition) - 07 Dec 11 (Release) - 04 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Type Iii Secretion System, Tip Protein, Deoxycholate, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. L. Barta, M. Guragain, P. Adam, N. E. Dickenson, M. Patil, B. V. Geisbrecht, W. L. Picking, W. D. Picking
Identification Of The Bile Salt Binding Site On Ipad From Shigella Flexneri And The Influence Of Ligand Binding On Ipad Structure.
Proteins V. 80 935 2012
PubMed-ID: 22423359 | Reference-DOI: 10.1002/PROT.23251

Molecule 1 - INVASIN IPAD
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	469008
	Fragment	:	UNP RESIDUES 39-322
	Gene	:	IPAD, CP0126
	Organism Scientific	:	SHIGELLA FLEXNERI
	Organism Taxid	:	623
	Synonym	:	36 KDA MEMBRANE ANTIGEN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	DXC	2	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	DXC	-1	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	DXC	2	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	DXC	2	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:129 , HIS B:131 , VAL B:314 , HOH B:377	BINDING SITE FOR RESIDUE DXC B 1
2	AC2	SOFTWARE	TRP B:135 , VAL B:312 , LEU B:315 , SER B:316	BINDING SITE FOR RESIDUE DXC B 323
3	AC3	SOFTWARE	SER A:173 , GLY A:176 , TRP A:177	BINDING SITE FOR RESIDUE GOL A 3968
4	AC4	SOFTWARE	ASN A:280 , SER A:284 , ASP A:287 , HOH A:418	BINDING SITE FOR RESIDUE GOL A 323
5	AC5	SOFTWARE	GLU A:286 , THR A:289 , HOH A:375 , HOH A:453	BINDING SITE FOR RESIDUE GOL A 324

(no "SS Bond" information available for 3R9V)

Asymmetric Unit

No.	Residues
1	Gly A:185	-	Asn A:186
2	Tyr A:212	-	Pro A:213
3	Tyr B:212	-	Pro B:213

Asymmetric Unit (7, 13)

								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	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)

Biological Unit 1 (7, 7)

								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	A	136	D
2	UniProt	VAR_IPAD_SHIFL_004 *	N	140	K	IPAD_SHIFL	---	---	A	N	140	K
3	UniProt	VAR_IPAD_SHIFL_005 *	D	144	N	IPAD_SHIFL	---	---	A	D	144	N
4	UniProt	VAR_IPAD_SHIFL_006 *	N	193	K	IPAD_SHIFL	---	---	A	N	193	K
5	UniProt	VAR_IPAD_SHIFL_007 *	Q	220	K	IPAD_SHIFL	---	---	A	Q	220	K
6	UniProt	VAR_IPAD_SHIFL_008 *	Q	239	E	IPAD_SHIFL	---	---	A	Q	239	E
7	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 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_IPAD_SHIFL_003 *	A	136	D	IPAD_SHIFL	---	---	B	A	136	D
2	UniProt	VAR_IPAD_SHIFL_004 *	N	140	K	IPAD_SHIFL	---	---	B	N	140	K
3	UniProt	VAR_IPAD_SHIFL_005 *	D	144	N	IPAD_SHIFL	---	---	B	D	144	N
5	UniProt	VAR_IPAD_SHIFL_007 *	Q	220	K	IPAD_SHIFL	---	---	B	Q	220	K
6	UniProt	VAR_IPAD_SHIFL_008 *	Q	239	E	IPAD_SHIFL	---	---	B	Q	239	E
7	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)

Biological Unit 3 (7, 13)

								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	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 3R9V)

(no "Exon" information available for 3R9V)

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:198
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:198
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        
           IPAD_SHIFL   122 ELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTI 319
               SCOP domains d3r9va_ A: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeehhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...eeeee....eeeee.hhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------D---K---N------------------------------------------------K--------------------------K------------------E-------N------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r9v A 122 ELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTI 319
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:193
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314   
           IPAD_SHIFL   125 GDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSS 317
               SCOP domains d3r9vb_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------------hhhhhhhhhhhh............hhhhhhhhhhhhh...eeeee....eeeee.hhhhhhhhhhhhhh......---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------D---K---N---------------------------------------------------------------------------K------------------E-------N---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r9v B 125 GDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSS---------------------LKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEV---------WNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSS 317
                                   134       144       154       164        |-         -         -|      204       214       224       234       244       254       264    |    -    |  284       294       304       314   
                                                                          173                   195                                                                       269       279

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	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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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)

1a	d3r9va_	A:
1b	d3r9vb_	B:

(no "CATH Domain" information available for 3R9V)

(no "Pfam Domain" information available for 3R9V)

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.

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	Cis Peptide Bonds
		Gly A:185 - Asn A:186	[ RasMol ]
		Tyr A:212 - Pro A:213	[ RasMol ]
		Tyr B:212 - Pro B:213	[ RasMol ]

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	3r9v
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	IPAD_SHIFL \| P18013
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	IPAD_SHIFL \| P18013	:	2j0n 2j0o 2jaa 4d3e

(no "Related Entries Specified in the PDB File" available for 3R9V)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 13)

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Exons (0, 0)

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