Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF DROSOPHILA DOPAMINE TRANSPORTER WITH SUBSITEB MUTATIONS (D121G/S426M) BOUND TO 3,4DICHLOROPHENETHYLAMINE
 
Authors :  A. Penmatsa, K. Wang, E. Gouaux
Date :  17 Jan 15  (Deposition) - 06 May 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Integral Membrane Protein, Neurotransmitter Transporter, Protein Transport-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 - TRANSPORTER
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Taxid: 9606
    Gene: DAT, CG8380
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
 
Molecule 2 - ANTIBODY FRAGMENT LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - ANTIBODY FRAGMENT HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
142J1Ligand/Ion2-(3,4-DICHLOROPHENYL)ETHANAMINE
2CL1Ligand/IonCHLORIDE ION
3CLR2Ligand/IonCHOLESTEROL
4N9S1Ligand/Ion4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSE
5NA3Ligand/IonSODIUM ION
6P4G1Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:43 , ALA A:44 , ASP A:46 , VAL A:120 , PHE A:319 , SER A:320 , PHE A:325 , GLY A:425binding site for residue 42J A 602
2AC2SOFTWAREALA A:44 , ASP A:46 , ASN A:49 , SER A:320 , ASN A:352binding site for residue NA A 603
3AC3SOFTWAREGLY A:42 , VAL A:45 , LEU A:417 , ASP A:420 , SER A:421binding site for residue NA A 604
4AC4SOFTWARETYR A:69 , GLN A:316 , SER A:320 , SER A:356binding site for residue CL A 605
5AC5SOFTWARELEU A:37 , LEU A:270 , TYR A:273 , ILE A:351binding site for residue CLR A 607
6AC6SOFTWAREARG A:133 , ALA A:137 , PRO A:144binding site for residue N9S A 608
7AC7SOFTWAREGLN L:6 , MET L:21 , THR L:22 , THR L:103binding site for residue NA L 301

(-) 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  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:95 -Pro L:96
3Tyr L:141 -Pro L:142
4Arg H:98 -Gly H:99
5Cys H:134 -Gly H:135
6Phe H:152 -Pro H:153
7Glu H:154 -Pro H:155
8Trp H:194 -Pro H:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XPH)

(-) 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:534
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............................hhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xph A  25 DERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVGFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFEGHVEGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAVLLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWVDAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGMEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYGLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRD 599
                                    34        44        54        64        74        84        94       104       114       124       134       144       154      |205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595    
                                                                                                                                                                  161|                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                   203                                                                                                                                                                                                                                                                                                                                                                                                            


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee........eeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xph H   1 EVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEVRQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


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.....eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeee.........eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xph L   1 ENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIEGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 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 4XPH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    42J  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CLR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    N9S  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P4G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg H:98 - Gly H:99   [ RasMol ]  
    Cys H:134 - Gly H:135   [ RasMol ]  
    Glu H:154 - Pro H:155   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:194 - Pro H:195   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
    Tyr L:95 - Pro L:96   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4xph
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DAT_DROME | Q7K4Y6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DAT_DROME | Q7K4Y6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4xpf 4xpg 4xpt

(-) Related Entries Specified in the PDB File

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