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(-) Description

Title :  STRUCTURAL BASIS OF MULTIPLE BINDING CAPACITY OF THE ACRB MULTIDRUG EFFLUX PUMP
 
Authors :  E. W. Yu, G. Medermott, H. I. Zgurskaya, H. Nikaido, D. E. Koshland Jr.
Date :  03 Apr 03  (Deposition) - 13 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. W. Yu, G. Mcdermott, H. I. Zgurskaya, H. Nikaido, D. E. Koshland
Structural Basis Of Multiple Drug-Binding Capacity Of The Acrb Multidrug Efflux Pump.
Science V. 300 976 2003
PubMed-ID: 12738864  |  Reference-DOI: 10.1126/SCIENCE.1083137

(-) Compounds

Molecule 1 - ACRIFLAVINE RESISTANCE PROTEIN B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ACRB OR ACRE OR B0462
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1DEQ1Ligand/IonDEQUALINIUM
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1DEQ3Ligand/IonDEQUALINIUM

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:99 , ALA A:385BINDING SITE FOR RESIDUE DEQ A 4001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OYD)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Ala A:305 -Ile A:306
2Ile A:306 -Arg A:307
3Arg A:307 -Ala A:308
4Ala A:308 -Glu A:309
5Glu A:309 -Leu A:310
6Thr A:993 -Gly A:994
7Ser A:997 -Gly A:998

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OYD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OYD)

(-) Exons   (0, 0)

(no "Exon" information available for 1OYD)

(-) 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:1006
 aligned with ACRB_ECOLI | P31224 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:1030
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036
          ACRB_ECOLI      7 DRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRK 1036
               SCOP domains d1oyda7 A:7-37,A:331-498       d1oyda1 A:38-134 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains d1oyda2 A:135-181,A:274-330                    d1oyda5 A:182-273                                                                           d1oyda2 A:135-181,A:274-330                              d1oyda7 A:7-37,A:331-498 Multidrug efflux transporter AcrB transmembrane domain                                                                                                       d1oyda8 A:513-566,A:869-1036                          d1oyda3 A:567-673 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains          d1oyda4 A:674-724,A:813-859                        d1oyda6 A:725-812                                                                       d1oyda4 A:674-724,A:813-859                             d1oyda8 A:513-566,A:869-1036 Multidrug efflux transporter AcrB transmembrane domain                                                                                      SCOP domains
               CATH domains 1oydA01 A:7-37,A:329-513       1oydA02 A:38-132,A:813-820 Multidrug efflux transporter AcrB pore domain                       1oydA03 A:133-179,A:276-328                    1oydA04 A:180-275 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains   1oydA03 A:133-179,A:276-328                          1oydA01 A:7-37,A:329-513 Multidrug efflux transporter AcrB transmembrane domain                                                                                                          1oydA05 A:514-568,A:870-1036                           1oydA06 A:569-673 Multidrug efflux transporter AcrB pore domain                                          1oydA07 A:674-723,A:821-869                       1oydA08 A:724-812                                                                        1oydA02 1oydA07 A:674-723,A:821-869                      1oydA05 A:514-568,A:870-1036 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.............eeeeeee.......hhhhhhhhhhhhh........eeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhh...hhhhhh...eeee....eee..eeee.......hhhhhhhh..hhhhhhhhhhh.eeee....eeeeeeehhhhhhh...hhhhhhhhhhhhh......ee............ee........hhhhhhh.eeeee...eeeehhhheeeeeee.....eee....eeeeeeee............................eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeee.....hhhhhhhhhhhhhhhhhh.....eee..eee..........eeeee.ee...........hhhhhhhhhhhhhh.....ee..................eeee.....hhhhhhhhhhhhhhhhhhh.-.............eeeee..hhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhh.hhhhhh...eee...eeehhhhhh.eeeee...eeeee..eeeeee.........hhhhhhhhhhhhh..........---------..hhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1oyd A    7 DRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLK--------------FGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHP-MLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDW---------SGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRK 1036
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496 |       -      |516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706   | | 716       726       736       746       756       766       776       786       796       806       816       826       836       846       856  |      -  |    876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     498            513                                                                                                                                                                                                  710 |                                                                                                                                                859       869                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           712
   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  (3, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (6, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OYD)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (ACRB_ECOLI | P31224)
molecular function
    GO:0015238    drug transmembrane transporter activity    Enables the directed movement of a drug from one side of a membrane to the other. A drug is any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0015307    drug:proton antiporter activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + drug(in) = H+(in) + drug(out).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
    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:0046618    drug export    The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, out of a cell or organelle.
    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: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:0005887    integral component of plasma membrane    The component of the plasma 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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  1oyd
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ACRB_ECOLI | P31224: 1iwg 1oy6 1oy8 1oy9 1oye 1t9t 1t9u 1t9v 1t9w 1t9x 1t9y 2dhh 2dr6 2drd 2gif 2hqc 2hqd 2hqf 2hqg 2hrt 2i6w 2j8s 2rdd 2w1b 3aoa 3aob 3aoc 3aod 3d9b 3noc 3nog 3w9h 4c48 4cdi 4dx5 4dx6 4dx7 4k7q 4u8v 4u8y 4u95 4u96 4zit 4ziv 4ziw 4zjl 4zjo 4zjq 4zlj 4zll 4zln 5en5 5eno 5enp 5enq 5enr 5ens 5ent 5jmn 5nc5 5ng5 5o66 5v5s

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1OYD)