1YC9 - JenaLib

Title :   THE CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN VCEC FROM THE BACTERIAL PATHOGEN VIBRIO CHOLERAE AT 1.8 RESOLUTION

Authors :   L. Federici, D. Du, F. Walas, H. Matsumura, J. Fernandez-Recio, K. S. Mc M. I. Borges-Walmsley, B. F. Luisi, A. R. Walmsley

Date :   22 Dec 04 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Vibrio Cholerae, Outer Membrane Protein, Multidrug Resistance, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Federici, D. Du, F. Walas, H. Matsumura, J. Fernandez-Recio, K. S. Mckeegan, M. I. Borges-Walmsley, B. F. Luisi, A. R. Walmsley
The Crystal Structure Of The Outer Membrane Protein Vcec From The Bacterial Pathogen Vibrio Cholerae At 1. 8 A Resolution
J. Biol. Chem. V. 280 15307 2005
PubMed-ID: 15684414 | Reference-DOI: 10.1074/JBC.M500401200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:411
 aligned with Q9KS51_VIBCH | Q9KS51 from UniProtKB/TrEMBL  Length:484

    Alignment length:418
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472        
         Q9KS51_VIBCH    63 WPSANWWQRYQDAQLNHLIEEALQHSPSLEMAMARLKGAQGFARQAGAIRSFDLGLAASATESKVSERYQSATPPDGWNDYGTLTLNFQYDFDFWGKNRAAVVAATSELAAAEAESVAARLMISTSIANAYAELARLYANQETVHAALQVRNKTVELLEKRYANGLETLGSVSQAKAVAASVEAELLGIQESIQLQKNALAALVGQGPDRAASIEEPHITLTSRYGLPSEAGVGLLGHRADITAARWRAEAAAQQVGIAQAQFYPDVTLSAFIGYQAFGLDHLFDSGNDAGAIGPAIYLPLFTGGRLEGQLTSAEARYQEAVAQYNGTLVQALYEVADVVTSSQALQARINKTEQAVQQAEQALHIATNRYQGGLATYLDVLVAEESLLNNQRALVNLQSRAFSLDLALIHALGGGFE 480
               SCOP domains d1yc9a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1yc9A01 A:63-112,A:159-326,A:364-479              1yc9A02 A:113-158,A:327-363                   1yc9A01 A:63-112,A:159-326,A:364-479 Outer membrane efflux proteins (OEP)                                                                                               1yc9A02 A:113-158,A:327-363          1yc9A01 A:63-112,A:159-326,A:364-479 Outer membrane efflux proteins (OEP)                                           - CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------OEP-1yc9A01 A:297-476                                                                                                                                                               ---- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------OEP-1yc9A02 A:297-476                                                                                                                                                               ---- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.............eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...........-------hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee.hhhh.....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yc9 A  63 WPSANWWQRYQDAQLNHLIEEALQHSPSLCMAMARLKGAQGFARQAGAIRSFDLGLAASATESKVSERYQSATPPDGWNDYGTLTLNFQYDFDFWGKNRAAVVAATSELAAAEAESVAARLMISTSIANAYAELARLYANQETVHAALQVRNKTVELLEKRYANGLETLGSVSQAKAVAASVEAELLGIQESIQLQKNALAALVGQGPDRAASIEEPHITLTSRY-------VGLLGHRADITAARWRAEAAAQQVGIAQAQFYPDVTLSAFIGYQAFGLDHLFDSGNDAGAIGPAIYLPLFTGGRLEGQLTSAEARYQEAVAQYNGTLVQALHEIADVVTSSQALQARINKTEQAVQQAEQALHIATNRYQGGLATYLDVLVAEESLLNNQRALVNLQSRAFSLDLALIHALGGGFE 480
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282    |    -  |    302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472        
                                                                                                                                                                                                                                                          287     295

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (Q9KS51_VIBCH | Q9KS51)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006855	drug transmembrane transport	The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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