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(-) Description

Title :  CRYSTAL STRUCTURE OF AN INWARD-FACING EUKARYOTIC ABC MULTIDRUG TRANSPORTER G277V/A278V/A279V MUTANT IN COMPLEX WITH AN CYCLIC PEPTIDE INHIBITOR, ACAP
 
Authors :  A. Kodan, T. Yamaguchi, T. Nakatsu, K. Sakiyama, C. J. Hipolito, A. Fuji R. Hirokane, K. Ikeguchi, B. Watanabe, J. Hirtake, Y. Kimura, H. Suga, H. Kato
Date :  18 Nov 13  (Deposition) - 30 Apr 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rec Fold, Multi Drug Transporter, Macrocyclic Peptide, Transport Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kodan, T. Yamaguchi, T. Nakatsu, K. Sakiyama, C. J. Hipolito, A. Fujioka, R. Hirokane, K. Ikeguchi, B. Watanabe, J. Hiratake, Y. Kimura, H. Suga, K. Ueda, H. Kato
Structural Basis For Gating Mechanisms Of A Eukaryotic P-Glycoprotein Homolog.
Proc. Natl. Acad. Sci. Usa V. 111 4049 2014
PubMed-ID: 24591620  |  Reference-DOI: 10.1073/PNAS.1321562111

(-) Compounds

Molecule 1 - ATP-BINDING CASSETTE, SUB-FAMILY B, MEMBER 1
    Chains: A
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: PABC3
    Expression System Strain: AD1-8U
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Fragment: TMD AND NBD DOMAIN, UNP RESIDUES 93-696
    Gene: CYME_CMD148C
    Mutation: YES
    Organism Scientific: CYANIDIOSCHYZON MEROLAE
    Organism Taxid: 45157
 
Molecule 2 - ANTI-CMABCB1 PEPTIDE
    Chains: B
    Engineered: YES
    Other Details: SELECTED BY THE RAPID SYSTEM PROTOCOL
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2DMU5Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
3DTR1Mod. Amino AcidD-TRYPTOPHAN
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:114 , THR A:119 , VAL A:122 , MET A:456 , DMU A:804BINDING SITE FOR RESIDUE DMU A 801
2AC2SOFTWAREGLY A:179 , ALA A:183BINDING SITE FOR RESIDUE DMU A 802
3AC3SOFTWAREARG A:107 , TRP A:114 , DMU A:801BINDING SITE FOR RESIDUE DMU A 804
4AC4SOFTWAREGLY A:471 , MET A:631 , ALA A:632 , SER A:633 , VAL A:636 , ASP A:652BINDING SITE FOR RESIDUE TRS A 805
5AC5SOFTWAREPHE B:8 , LEU B:14BINDING SITE FOR RESIDUE DMU B 101
6AC6SOFTWAREARG A:144 , LYS A:162 , TYR A:163 , ILE A:257 , ASN A:375 , ASN A:378 , DMU B:101BINDING SITE FOR CHAIN B OF ANTI-CMABCB1 PEPTIDE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WMG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WMG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WMG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WMG)

(-) Exons   (0, 0)

(no "Exon" information available for 3WMG)

(-) Sequences/Alignments

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:589
 aligned with M1VAN7_CYAM1 | M1VAN7 from UniProtKB/TrEMBL  Length:696

    Alignment length:589
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681         
         M1VAN7_CYAM1   102 TGVTARRIFALAWSSSATMIVIGFIASILEGATLPAFAIVFGRMFQVFTKSKSQIEGETWKYSVGFVGIGVFEFIVAGSRTALFGIASERLARDLRVAAFSNLVEQDVTYFDRRKAGELGGKLNNDVQVIQYSFSKLGAVLFNLAQCVVGIIVAFIFAPALTGVLIALSPLVVLAGAAQMIEMSGNTKRSSEAYASAGSVAAEVFSNIRTTKAFEAERYETQRYGSKLDPLYRLGRRRYISDGLFFGLSMLVIFCVYALALWWGGQLIARGSLNLGNLLTAFFSAILGFMGVGQAAQVWPDVTRGLGAGGELFAMIDRVPQYRRPDPGAEVVTQPLVLKQGIVFENVHFRYPTRMNVEVLRGISLTIPNGKTVAIVGGSGAGKSTIIQLLMRFYDIEPQGGGLLLFDGTPAWNYDFHALRSQIGLVSQEPVLFSGTIRDNILYGKRDATDEEVIQALREANAYSFVMALPDGLDTEVGERGLALSGGQKQRIAIARAILKHPTLLCLDESTSALDAESEALVQEALDRMMASDGVTSVVIAHRLSTVARADLILVMQDGVVVEQGNHSELMALGPSGFYYQLVEKQLAS 690
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................eeeeeeeee..........eeeeeeeee...eeeeee.hhhhhhhhhhhhh...........eeee..ee.hhhhhhhhhh.eeee........eehhhhhhh.....hhhhhhhhhhhh.hhhhhhh..hhhh.ee.......hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh.eeeeee..eeeeeehhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wmg A 102 TGVTARRIFALAWSSSATMIVIGFIASILEGATLPAFAIVFGRMFQVFTKSKSQIEGETWKYSVGFVGIGVFEFIVAGSRTALFGIASERLARDLRVAAFSNLVEQDVTYFDRRKAGELGGKLNNDVQVIQYSFSKLGAVLFNLAQCVVGIIVAFIFAPALTGVLIALSPLVVLAVVVQMIEMSGNTKRSSEAYASAGSVAAEVFSNIRTTKAFEAERYETQRYGSKLDPLYRLGRRRYISDGLFFGLSMLVIFCVYALALWWGGQLIARGSLNLGNLLTAFFSAILGFMGVGQAAQVWPDVTRGLGAGGELFAMIDRVPQYRRPDPGAEVVTQPLVLKQGIVFENVHFRYPTRMNVEVLRGISLTIPNGKTVAIVGGSGAGKSTIIQLLMRFYDIEPQGGGLLLFDGTPAWNYDFHALRSQIGLVSQEPVLFSGTIRDNILYGKRDATDEEVIQALREANAYSFVMALPDGLDTEVGERGLALSGGQKQRIAIARAILKHPTLLCLDESTSALDAESEALVQEALDRMMASDGVTSVVIAHRLSTVARADLILVMQDGVVVEQGNHSELMALGPSGFYYQLVEKQLAS 690
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681         


Chain B from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 3wmg B   0 xxLDQIVWFNAPGDLHLC  17
                            ||       9        
                            0-ACE             
                             1-DTR
   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  (0, 0)

(no "SCOP Domain" information available for 3WMG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WMG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WMG)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (M1VAN7_CYAM1 | M1VAN7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042626    ATPase activity, coupled to transmembrane movement of substances    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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        M1VAN7_CYAM1 | M1VAN7: 3wme 3wmf

(-) Related Entries Specified in the PDB File

3wme 3wmf