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(-) Description

Title :  X-RAY STRUCTURE OF DROSOPHILA DOPAMINE TRANSPORTER WITH SUBSITEB MUTATIONS (D121G/S426M) BOUND TO RTI-55
 
Authors :  A. Penmatsa, K. H. Wang, E. Gouaux
Date :  16 Jan 15  (Deposition) - 06 May 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.27
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  All Alpha-Helical Integral Membrane Protein, Transport Protein- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Wang, A. Penmatsa, E. Gouaux
Neurotransmitter And Psychostimulant Recognition By The Dopamine Transporter.
Nature V. 521 322 2015
PubMed-ID: 25970245  |  Reference-DOI: 10.1038/NATURE14431

(-) Compounds

Molecule 1 - DOPAMINE TRANSPORTER-PROTEIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: GNTI-, HEK293S
    Expression System Plasmid: PEG BACMAM
    Expression System Taxid: 9606
    Gene: DDAT
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
 
Molecule 2 - ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA CELLS
 
Molecule 3 - ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA CELLS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
142F1Ligand/IonMETHYL (1R,2S,3S,5S)-3-(4-IODOPHENYL)-8-METHYL-8-AZABICYCLO[3.2.1]OCTANE-2-CARBOXYLATE
2CL1Ligand/IonCHLORIDE ION
3CLR2Ligand/IonCHOLESTEROL
4DMU1Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
5NA2Ligand/IonSODIUM ION
6P4G1Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:133 , PHE A:136 , TYR A:219 , ASP A:238 , ARG L:156binding site for residue DMU A 701
2AC2SOFTWAREPHE A:43 , ASP A:46 , VAL A:120 , GLY A:121 , TYR A:123 , TYR A:124 , ASN A:125 , SER A:422 , GLY A:425binding site for residue 42F A 703
3AC3SOFTWAREPHE A:350 , TRP A:519binding site for residue CLR A 704
4AC4SOFTWARETYR A:273 , LEU A:277 , ILE A:351binding site for residue CLR A 705
5AC5SOFTWAREALA A:44 , ASP A:46 , ASN A:49 , SER A:320 , ASN A:352binding site for residue NA A 706
6AC6SOFTWAREGLY A:42 , VAL A:45 , LEU A:417 , ASP A:420 , SER A:421binding site for residue NA A 707
7AC7SOFTWARETYR A:69 , GLN A:316 , SER A:320 , SER A:356binding site for residue CL A 708

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:148 -A:157
2H:22 -H:96
3H:146 -H:201
4L:23 -L:89
5L:135 -L:195

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:95 -Pro L:96
3Tyr L:141 -Pro L:142
4Pro H:132 -Val H:133
5Phe H:152 -Pro H:153
6Glu H:154 -Pro H:155
7Trp H:194 -Pro H:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XPF)

(-) 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:532
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.........ee.......ee.hhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xpf A  25 DERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVGFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAVLLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWVDAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGMEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYGLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRD 599
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597  
                                                                                                                                                                    163|                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                                     207                                                                                                                                                                                                                                                                                                                                                                                                        


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee........eeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee..hhhhh..ee...eeeee........eeeee......eeeeeeeeeee.....eeee........eee...ee....eeeeeeeeee.hhhhhh..eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xpf H   1 EVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEVRQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  144       154       164       174       184       194       204       214     
                                                                                                                                                               134|                                                                                
                                                                                                                                                                139                                                                                


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee....eeeeee......eeee.............eeeeeeeeeeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeee........eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xpf L   1 ENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4XPF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4xpf
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAT_DROME | Q7K4Y6: 4m48 4xnu 4xnx 4xp1 4xp4 4xp5 4xp6 4xp9 4xpa 4xpb 4xpg 4xph 4xpt

(-) Related Entries Specified in the PDB File

4xnu 4xnx 4xp1 4xp4 4xp5 4xp6 4xp9 4xpa 4xpb 4xpg 4xph 4xpt