2W5P - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   DRAE ADHESIN IN COMPLEX WITH CHLORAMPHENICOL SUCCINATE ( MONOCLINIC FORM)

Authors :   D. M. Pettigrew, P. Roversi, S. G. Davies, A. J. Russell, S. M. Lea

Date :   11 Dec 08 (Deposition) - 02 Jun 09 (Release) - 02 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Upec, Drae, Daec, Adhesin, Fimbrium, Haemagglutinin, Cell Projection, Fimbrial Adhesin, Chloramphenicol Succinate, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Pettigrew, P. Roversi, S. G. Davies, A. J. Russell, S. M. Lea
A Structural Study Of The Interaction Between The Dr Haemagglutinin Drae And Derivatives Of Chloramphenicol
Acta Crystallogr. , Sect. D V. 65 513 2009
PubMed-ID: 19465765 | Reference-DOI: 10.1107/S0907444909005113

Molecule 1 - DR HEMAGGLUTININ STRUCTURAL SUBUNIT
	Cell Line	:	M15
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-30
	Expression System Taxid	:	562
	Fragment	:	ADHESIN SUBUNIT, RESIDUES 23-160
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	IH11128
	Synonym	:	DRAE HAEMAGGLUTININ
	Variant	:	O75:K5:H

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CL8	3	Ligand/Ion	CHLORAMPHENICOL SUCCINATE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:40 , GLY A:42 , GLY A:113 , ILE A:114 , TYR A:115	BINDING SITE FOR RESIDUE CL8 A 143
2	AC2	SOFTWARE	GLY A:24 , ASP A:25 , HOH A:2114 , HOH A:2115 , THR C:8 , GLY C:9 , THR C:10	BINDING SITE FOR RESIDUE SO4 A 159
3	AC3	SOFTWARE	PRO B:40 , GLY B:42 , PRO B:43 , GLY B:113 , ILE B:114 , TYR B:115	BINDING SITE FOR RESIDUE CL8 B 143
4	AC4	SOFTWARE	THR A:8 , GLY A:9 , THR A:10 , GLY B:24 , ASP B:25 , HOH B:2022	BINDING SITE FOR RESIDUE SO4 B 159
5	AC5	SOFTWARE	PRO C:40 , GLY C:42 , PRO C:43 , GLY C:113 , ILE C:114 , TYR C:115	BINDING SITE FOR RESIDUE CL8 C 143
6	AC6	SOFTWARE	GLY B:9 , THR B:10 , GLY C:24 , ASP C:25 , HOH C:2118	BINDING SITE FOR RESIDUE SO4 C 159

Asymmetric/Biological Unit

No.	Residues
1	A:19	-	C:51
2	A:51	-	B:19
3	B:51	-	C:19

Asymmetric/Biological Unit

No.	Residues
1	Ala A:138	-	Lys A:139
2	Ala B:138	-	Lys B:139

Asymmetric/Biological Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DRAA_ECOLX_001 *	R	43	Y	DRAA_ECOLX	---	---	A/B/C	R	22	Y
	* ID not provided by source

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

(no "PROSITE Motif" information available for 2W5P)

(no "Exon" information available for 2W5P)

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:140
 aligned with DRAA_ECOLX | P24093 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:140
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160
           DRAA_ECOLX    21 AGFTPSGTTGTTKLTVTEECQVRVGDLTVAKTRGQLTDAAPIGPVTVQALGCDARQVALKADTDNFEQGKFFLISDNNRDKLYVNIRPTDNSAWTTDNGVFYKNDVGSWGGIIGIYVDGQQTNTPPGNYTLTLTGGYWAK 160
               SCOP domains d2w5pa_ A: DraA/Afimbrial adhesin Afa-III                                                                                                    SCOP domains
               CATH domains 2w5pA00 A:0-139 Afimbrial adhesin afa-iii.                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee...eeee.....eee.hhh....eeeeeeeeee...................eeeeee.....eeeeeeee.....................eeeeeeee.........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------Y--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w5p A   0 GSFTPSGTTGTTKLTVTEKCQVRVGDLTVAKTRGQLTDAAPIGPVTVQALGCDARQVALKADTDNFEQGKFFLISDNNRDKLYVNIRPTDNSAWTTDNGVFYKNDVGSWGGIIGIYVDGQQTNTPPGNYTLTLTGGYWAK 139
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with DRAA_ECOLX | P24093 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:140
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160
           DRAA_ECOLX    21 AGFTPSGTTGTTKLTVTEECQVRVGDLTVAKTRGQLTDAAPIGPVTVQALGCDARQVALKADTDNFEQGKFFLISDNNRDKLYVNIRPTDNSAWTTDNGVFYKNDVGSWGGIIGIYVDGQQTNTPPGNYTLTLTGGYWAK 160
               SCOP domains d2w5pb_ B: DraA/Afimbrial adhesin Afa-III                                                                                                    SCOP domains
               CATH domains 2w5pB00 B:0-139 Afimbrial adhesin afa-iii.                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee...eeee.....eee.hhh....eeeeeeeeee...................eeeeee.....eeeeeeee.....................eeeeeeee.........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------Y--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w5p B   0 GSFTPSGTTGTTKLTVTEKCQVRVGDLTVAKTRGQLTDAAPIGPVTVQALGCDARQVALKADTDNFEQGKFFLISDNNRDKLYVNIRPTDNSAWTTDNGVFYKNDVGSWGGIIGIYVDGQQTNTPPGNYTLTLTGGYWAK 139
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with DRAA_ECOLX | P24093 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:140
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160
           DRAA_ECOLX    21 AGFTPSGTTGTTKLTVTEECQVRVGDLTVAKTRGQLTDAAPIGPVTVQALGCDARQVALKADTDNFEQGKFFLISDNNRDKLYVNIRPTDNSAWTTDNGVFYKNDVGSWGGIIGIYVDGQQTNTPPGNYTLTLTGGYWAK 160
               SCOP domains d2w5pc_ C: DraA/Afimbrial adhesin Afa-III                                                                                                    SCOP domains
               CATH domains 2w5pC00 C:0-139 Afimbrial adhesin afa-iii.                                                                                                   CATH domains
           Pfam domains (1) --Adhesin_Dr-2w5pC01 C:2-139                                                                                                                 Pfam domains (1)
           Pfam domains (2) --Adhesin_Dr-2w5pC02 C:2-139                                                                                                                 Pfam domains (2)
           Pfam domains (3) --Adhesin_Dr-2w5pC03 C:2-139                                                                                                                 Pfam domains (3)
         Sec.struct. author .eeeeeeeeeeeeeeee...eeee.....eee.hhh....eeeeeeeeee............hhh..--.eeeee.....eeeeeeee.....................eeeeeeee.........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------Y--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w5p C   0 GSFTPSGTTGTTKLTVTEKCQVRVGDLTVAKTRGQLTDAAPIGPVTVQALGCDARQVALKADTDNFE--KFFLISDNNRDKLYVNIRPTDNSAWTTDNGVFYKNDVGSWGGIIGIYVDGQQTNTPPGNYTLTLTGGYWAK 139
                                     9        19        29        39        49        59      | 69        79        89        99       109       119       129       139
                                                                                             66 69

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 beta proteins (24004)

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

Superfamily: Bacterial adhesins (93)

Family: Dr-family adhesin (11)

Protein domain: DraA/Afimbrial adhesin Afa-III (11)

Escherichia coli [TaxId: 562] (11)

1a	d2w5pa_	A:
1b	d2w5pb_	B:
1c	d2w5pc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Afimbrial adhesin afa-iii. (12)

Escherichia coli. Organism_taxid: 562. Strain: ih11128. Variant: o75:k5:h. Cell_line: m15. (4)

1a	2w5pA00	A:0-139
1b	2w5pB00	B:0-139
1c	2w5pC00	C:0-139

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Adhesin (36)

Family: Adhesin_Dr (9)

Escherichia coli (9)

1a	Adhesin_Dr-2w5pC01	C:2-139
1b	Adhesin_Dr-2w5pC02	C:2-139
1c	Adhesin_Dr-2w5pC03	C:2-139

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DRAA_ECOLX | P24093)

cellular component
	GO:0009289		pilus		A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:138 - Lys A:139	[ RasMol ]
		Ala B:138 - Lys B:139	[ RasMol ]

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	2w5p
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UniProtKB/Swiss-Prot
	DRAA_ECOLX \| P24093	:	1usq 1ut1 2jkj 2jkl 2jkn

1usq	COMPLEX OF E. COLI DRAE ADHESIN WITH CHLORAMPHENICOL
1ut1	DRAE ADHESIN FROM ESCHERICHIA COLI
2jkj	DRAE ADHESIN IN COMPLEX WITH CHLORAMPHENICOL SUCCINATE
2jkl	DRAE ADHESIN IN COMPLEX WITH BROMAMPHENICOL
2jkn	DRAE ADHESIN IN COMPLEX WITH CHLORAMPHENICOL SUCCINATE (TRIGONAL FORM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (1, 3)

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