2WQX - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   INLB321_4R: S199R, D200R, G206R, A227R, C242A MUTANT OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN

Authors :   H. H. Niemann, D. M. Ferraris, D. W. Heinz

Date :   27 Aug 09 (Deposition) - 10 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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

Keywords :   Hgf Receptor Ligand, Leucine-Rich Repeat, Leucine Rich Repeat, Lrr, C-Met Ligand, Cell Invasion, Virulence Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Ferraris, E. Gherardi, Y. Di, D. W. Heinz, H. H. Niemann
Ligand-Mediated Dimerization Of The Met Receptor Tyrosine Kinase By The Bacterial Invasion Protein Inlb.
J. Mol. Biol. V. 395 522 2010
PubMed-ID: 19900460 | Reference-DOI: 10.1016/J.JMB.2009.10.074

Molecule 1 - INTERNALIN B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	CODONPLUS
	Expression System Vector Type	:	PLASMID
	Fragment	:	INTERNALIN DOMAIN, RESIDUES 36-321
	Mutation	:	YES
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	169963
	Other Details	:	RESIDUES 36-321 OF LISTERIA MONOCYTOGENES INLB 4R MUTANT
	Strain	:	EGD-E
	Synonym	:	INLB

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2WQX)

(no "Site" information available for 2WQX)

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

Asymmetric Unit

No.	Residues
1	Lys A:280	-	Pro A:281
2	Lys B:280	-	Pro B:281

(no "SAP(SNP)/Variant" information available for 2WQX)

Asymmetric Unit (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	INLB_LISMO	99-120 121-142 143-164 165-186 187-208 209-230	12	A:99-120 B:99-120 A:121-142 B:121-142 A:143-164 B:143-164 A:165-186 B:165-186 A:187-208 B:187-208 A:209-230 B:209-230

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	INLB_LISMO	99-120 121-142 143-164 165-186 187-208 209-230	6	A:99-120 - A:121-142 - A:143-164 - A:165-186 - A:187-208 - A:209-230 -

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	INLB_LISMO	99-120 121-142 143-164 165-186 187-208 209-230	6	- B:99-120 - B:121-142 - B:143-164 - B:165-186 - B:187-208 - B:209-230

(no "Exon" information available for 2WQX)

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:286
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:286
                                    45        55        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      
           INLB_LISMO    36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
               SCOP domains d2wqxa1 A:36-240 automated matches                                                                                                                                                                           d2wqxa2 A:241-321 automated matches                                               SCOP domains
               CATH domains 2wqxA01 A:36-245 Ribonuclease Inhibitor                                                                                                                                                                           2wqxA02 A:246-321  [code=2.60.40.1220, no name defined]                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eehhhhh.hhhhhhhhhhhh.......eehhhhhhh..eee...................eee........hhhhh.......ee........hhhhh......eee...................eee........hhhhhhh....eee........hhhhh......eee........hhhhh......eee.....ee...ee...eeeee.....................ee..eeeee.............eeee....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------LRR  PDB: A:99-120    LRR  PDB: A:121-142   LRR  PDB: A:143-164   LRR  PDB: A:165-186   LRR  PDB: A:187-208   LRR  PDB: A:209-230   ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wqx A  36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQIRRIVPLARLTKLQNLYLSKNHISDLRALRGLKNLDVLELFSQEALNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
                                    45        55        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

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:286
                                    45        55        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      
           INLB_LISMO    36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
               SCOP domains d2wqxb1 B:36-240 automated matches                                                                                                                                                                           d2wqxb2 B:241-321 automated matches                                               SCOP domains
               CATH domains 2wqxB01 B:36-245 Ribonuclease Inhibitor                                                                                                                                                                           2wqxB02 B:246-321  [code=2.60.40.1220, no name defined]                      CATH domains
           Pfam domains (1) Internalin_N-2wqxB07    --------------------------------------------------------------------------------------------------------LRR_4-2wqxB01 B:164-206                    LRR_6-2wqxB05 B:207-233    ------------------------------LRR_adjacent-2wqxB09 B:264-321                             Pfam domains (1)
           Pfam domains (2) Internalin_N-2wqxB08    --------------------------------------------------------------------------------------------------------LRR_4-2wqxB02 B:164-206                    LRR_6-2wqxB06 B:207-233    ------------------------------LRR_adjacent-2wqxB10 B:264-321                             Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------LRR_4-2wqxB03 B:164-206                    ------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------LRR_4-2wqxB04 B:164-206                    ------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ......eehhhhh.hhhhhhhhhhhh.......eehhhhhhh..eee...................eee........hhhhh.......ee........hhhhh......eee...................eee........hhhhhhh....eee........hhhhh......eee........hhhhh......eee.....ee...ee...eeeee.....................ee..eeeee.............eeee....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------LRR  PDB: B:99-120    LRR  PDB: B:121-142   LRR  PDB: B:143-164   LRR  PDB: B:165-186   LRR  PDB: B:187-208   LRR  PDB: B:209-230   ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wqx B  36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQIRRIVPLARLTKLQNLYLSKNHISDLRALRGLKNLDVLELFSQEALNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
                                    45        55        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

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LRR (77)

Family: LRR_4 (28)

Listeria monocytogenes (18)

1a	LRR_4-2wqxB01	B:164-206
1b	LRR_4-2wqxB02	B:164-206
1c	LRR_4-2wqxB03	B:164-206
1d	LRR_4-2wqxB04	B:164-206

Family: LRR_6 (24)

Listeria monocytogenes (10)

2a	LRR_6-2wqxB05	B:207-233
2b	LRR_6-2wqxB06	B:207-233

Clan: no clan defined [family: Internalin_N] (18)

Family: Internalin_N (18)

Listeria monocytogenes (18)

3a	Internalin_N-2wqxB07	B:36-59
3b	Internalin_N-2wqxB08	B:36-59

Clan: no clan defined [family: LRR_adjacent] (15)

Family: LRR_adjacent (15)

Listeria monocytogenes (15)

4a	LRR_adjacent-2wqxB09	B:264-321
4b	LRR_adjacent-2wqxB10	B:264-321

Asymmetric Unit(hide GO term definitions)

Chain A,B (INLB_LISMO | P25147)

molecular function
	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).

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2wqx)

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

	Cis Peptide Bonds
		Lys A:280 - Pro A:281	[ RasMol ]
		Lys B:280 - Pro B:281	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2wqx
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		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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	INLB_LISMO \| P25147
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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1d0b	INTERNALIN B LEUCINE RICH REPEAT DOMAIN
1h6t	INTERNALIN B: CRYSTAL STRUCTURE OF FUSED N- TERMINAL DOMAINS.
1m9s	CRYSTAL STRUCTURE OF INTERNALIN B (INLB), A LISTERIAMONOCYTOGENES VIRULENCE PROTEIN CONTAINING SH3-LIKEDOMAINS.
1otm	CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
1otn	CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
1oto	CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
2uzx	STRUCTURE OF THE HUMAN RECEPTOR TYROSINE KINASE MET IN COMPLEX WITH THE LISTERIA MONOCYTOGENES INVASION PROTEIN INLB: CRYSTAL FORM I
2uzy	STRUCTURE OF THE HUMAN RECEPTOR TYROSINE KINASE MET IN COMPLEX WITH THE LISTERIA MONOCYTOGENES INVASION PROTEIN INLB: LOW RESOLUTION, CRYSTAL FORM II
2wqu	INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: TRICLINIC CRYSTAL FORM
2wqv	INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: RHOMBOHEDRAL CRYSTAL FORM
2wqw	DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 12)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (4, 10)

Gene Ontology (1, 1)

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