4AVH - JenaLib

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Title :   STRUCTURE OF THE FIMH LECTIN DOMAIN IN THE TRIGONAL SPACE GROUP, IN COMPLEX WITH A THIOALKYL ALPHA-D-MANNOSIDE AT 2.1 A RESOLUTION

Authors :   A. Wellens, M. Lahmann, M. Touaibia, J. Vaucher, S. Oscarson, R. Roy, H. J. Bouckaert

Date :   26 May 12 (Deposition) - 27 Jun 12 (Release) - 05 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Cell Adhesion, Bacterial Adhesin, Type 1 Fimbriae, Urinary Tract Infection, Variable Immunoglobulin Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Wellens, M. Lahmann, M. Touaibia, J. Vaucher, S. Oscarson, R. Roy, H. Remaut, J. Bouckaert
The Tyrosine Gate As A Potential Entropic Lever In The Receptor-Binding Site Of The Bacterial Adhesin Fimh.
Biochemistry V. 51 4790 2012
PubMed-ID: 22657089 | Reference-DOI: 10.1021/BI300251R

Molecule 1 - FIMH
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	C43
	Expression System Vector	:	PET24A
	Expression System Vector Type	:	PLASMID
	Fragment	:	LECTIN DOMAIN, RESIDUES 10-167
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	364106
	Strain	:	UTI89

		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 (3, 5)

No.	Name	Count	Type	Full Name
1	FK9	2	Ligand/Ion	PROPYL THIOPROPYL ALPHA-D-MANNOPYRANOSIDE
2	NI	2	Ligand/Ion	NICKEL (II) ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FK9	1	Ligand/Ion	PROPYL THIOPROPYL ALPHA-D-MANNOPYRANOSIDE
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FK9	1	Ligand/Ion	PROPYL THIOPROPYL ALPHA-D-MANNOPYRANOSIDE
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:1 , ILE A:13 , ASN A:46 , ASP A:47 , TYR A:48 , ASP A:54 , GLN A:133 , ASN A:135 , ASP A:140 , PHE A:142 , HOH A:2001 , HOH A:2195	BINDING SITE FOR RESIDUE FK9 A 201
2	AC2	SOFTWARE	HIS A:45 , ASP A:47 , HOH A:2091 , HOH A:2092 , HOH A:2208	BINDING SITE FOR RESIDUE NI A 301
3	AC3	SOFTWARE	PHE B:1 , ILE B:13 , ASN B:46 , ASP B:47 , TYR B:48 , THR B:51 , ILE B:52 , ASP B:54 , GLN B:133 , ASN B:135 , TYR B:137 , ASP B:140 , HOH B:2001	BINDING SITE FOR RESIDUE FK9 B 201
4	AC4	SOFTWARE	HIS B:45 , ASP B:47 , HOH B:2075 , HOH B:2077 , HOH B:2078 , HOH B:2168	BINDING SITE FOR RESIDUE NI B 301
5	AC5	SOFTWARE	GLN A:59 , ARG A:60 , HOH A:2109 , HOH A:2111 , LYS B:4	BINDING SITE FOR RESIDUE SO4 A1159

Asymmetric Unit

No.	Residues
1	A:3	-	A:44
2	B:3	-	B:44

Asymmetric Unit

No.	Residues
1	Phe A:84	-	Pro A:85
2	Phe B:84	-	Pro B:85

(no "SAP(SNP)/Variant" information available for 4AVH)

(no "PROSITE Motif" information available for 4AVH)

(no "Exon" information available for 4AVH)

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:158
 aligned with A2IC68_ECOLX | A2IC68 from UniProtKB/TrEMBL  Length:227

    Alignment length:158
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
         A2IC68_ECOLX    10 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 167
               SCOP domains d4avha_ A: Mannose-specific adhesin FimH                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeeeehhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee.....eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4avh A   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain A from PDB  Type:PROTEIN  Length:158
 aligned with FIMH_ECOLI | P08191 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:158
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
           FIMH_ECOLI    22 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 179
               SCOP domains d4avha_ A: Mannose-specific adhesin FimH                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeeeehhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee.....eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4avh A   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with A2IC68_ECOLX | A2IC68 from UniProtKB/TrEMBL  Length:227

    Alignment length:158
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
         A2IC68_ECOLX    10 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 167
               SCOP domains d4avhb_ B: Mannose-specific adhesin FimH                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeeeehhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee.....eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4avh B   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with FIMH_ECOLI | P08191 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:158
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
           FIMH_ECOLI    22 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 179
               SCOP domains d4avhb_ B: Mannose-specific adhesin FimH                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeeeehhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee.....eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4avh B   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: Bacterial adhesins (93)

Family: Pilus subunits (59)

Protein domain: Mannose-specific adhesin FimH (22)

Escherichia coli [TaxId: 562] (22)

1a	d4avha_	A:
1b	d4avhb_	B:

(no "CATH Domain" information available for 4AVH)

(no "Pfam Domain" information available for 4AVH)

Asymmetric Unit(hide GO term definitions)

Chain A,B (A2IC68_ECOLX | A2IC68)

biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
cellular component
	GO:0009289	pilus	A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Chain A,B (FIMH_ECOLI | P08191)

molecular function
	GO:0005537	mannose binding	Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
	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:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
cellular component
	GO:0009289	pilus	A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Phe A:84 - Pro A:85	[ RasMol ]
		Phe B:84 - Pro B:85	[ RasMol ]

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

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	4avh
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	FIMH_ECOLI \| P08191
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	FIMH_ECOLI \| P08191
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4att	FIMH LECTIN DOMAIN CO-CRYSTAL WITH A ALPHA-D- MANNOSIDE O-LINKED TO A PROPYNYL PARA METHOXY PHENYL
4auj	FIMH LECTIN DOMAIN CO-CRYSTAL WITH A ALPHA-D- MANNOSIDE O-LINKED TO PARA HYDROXYPROPARGYL PHENYL
4auu	CRYSTAL STRUCTURE OF APO FIMH LECTIN DOMAIN AT 1.5 A RESOLUTION
4auy	STRUCTURE OF THE FIMH LECTIN DOMAIN IN THE TRIGONAL SPACE GROUP, IN COMPLEX WITH AN HYDROXYL PROPYNYL PHENYL ALPHA-D-MANNOSIDE AT 2.1 A RESOLUTION
4av0	STRUCTURE OF THE FIMH LECTIN DOMAIN IN THE TRIGONAL SPACE GROUP, IN COMPLEX WITH A METHOXY PHENYL PROPYNYL ALPHA-D-MANNOSIDE AT 2.1 A RESOLUTION
4av4	FIMH LECTIN DOMAIN CO-CRYSTAL WITH A ALPHA-D- MANNOSIDE O-LINKED TO A PROPYNYL PYRIDINE
4av5	STRUCTURE OF A TRICLINIC CRYSTAL OF THE FIMH LECTIN DOMAIN IN COMPLEX WITH A PROPYNYL BIPHENYL ALPHA-D- MANNOSIDE, AT 1.4 A RESOLUTION
4avi	STRUCTURE OF THE FIMH LECTIN DOMAIN IN THE TRIGONAL SPACE GROUP, IN COMPLEX WITH A METHYL ESTER OCTYL ALPHA-D-MANNOSIDE AT 2.4 A RESOLUTION
4avj	STRUCTURE OF THE FIMH LECTIN DOMAIN IN THE TRIGONAL SPACE GROUP, IN COMPLEX WITH A METHANOL TRIAZOL ETHYL PHENYL ALPHA-D-MANNOSIDE AT 2.1 A RESOLUTION
4avk	STRUCTURE OF TRIGONAL FIMH LECTIN DOMAIN CRYSTAL SOAKED WITH AN ALPHA-D-MANNOSIDE O-LINKED TO PROPYNYL PYRIDINE AT 2.4A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 6)

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