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(-) Description

Title :  CRYSTAL STRUCTURE OF A SUBSTRATE-FREE GLUTAMATE TRANSPORTER HOMOLOGUE FROM THERMOCOCCUS KODAKARENSIS
 
Authors :  A. Guskov, S. Jensen, S. Rempel, I. Hanelt, D. J. Slotboom
Date :  28 May 13  (Deposition) - 11 Sep 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Amino Acid Transporter, Aspartate Transport, Glutamate Transport Homologue, Transport Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Jensen, A. Guskov, S. Rempel, I. Hanelt, D. J. Slotboom
Crystal Structure Of A Substrate-Free Aspartate Transporter
Nat. Struct. Mol. Biol. V. 20 1224 2013
PubMed-ID: 24013209  |  Reference-DOI: 10.1038/NSMB.2663

(-) Compounds

Molecule 1 - PROTON/GLUTAMATE SYMPORTER, SDF FAMILY
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TK0986
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1PG44Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:82 , LYS A:86 , PHE A:256 , THR A:419 , ASN B:174BINDING SITE FOR RESIDUE PG4 A 501
2AC2SOFTWAREPRO B:77BINDING SITE FOR RESIDUE PG4 B 501
3AC3SOFTWARELEU C:30 , GLY C:223 , VAL C:226BINDING SITE FOR RESIDUE PG4 C 501
4AC4SOFTWARELEU C:198 , ARG C:289BINDING SITE FOR RESIDUE PG4 C 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KY0)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Asp A:11 -Tyr A:12
2Asn A:114 -Val A:115
3Gly A:122 -Lys A:123
4Leu B:10 -Asp B:11
5Asn B:114 -Val B:115
6Pro B:379 -Gly B:380
7Glu B:422 -Leu B:423
8Asp C:11 -Tyr C:12
9Asn C:114 -Val C:115
10Glu C:422 -Leu C:423

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KY0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KY0)

(-) Exons   (0, 0)

(no "Exon" information available for 4KY0)

(-) 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ky0a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ky0 A   9 YLDYPVLWKILWGLVLGAVFGLIAGHFGYAGAVKTYIKPFGDLFVRLLKMLVMPIVLASLVVGAASISPARLGRVGVKIVVYYLATSAMAVFFGLIVGRLFNVGANVNLGSGTGKAILVQTLLNIVPTNPFASLAKGEVLPVIFFAIILGIAITYLMNRNEERVRKSAETLLRVFDGLAEAMYLIVGGVMQYAPIGVFALIAYVMAEQGVRVVGPLAKVVGAVYTGLFLQIVITYFILLKVFGIDPIKFIRKAKDAMITAFVTRSSSGTLPVTMRVAEEEMGVDKGIFSFTLPLGATINMDGTALYQGVTVLFVANAIGHPLTLGQQLVVVLTAVLASIGTAGVPGAGAIMLAMVLQSVGLDLTPGSPVALAYAMILGIDAILDMGRTMVNVTGDLAGTVIVAKTEKELDESKWIS 430
                                    18        28        38        48        58        68        78        88        98       108       118      |134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424      
                                                                                                                                              125|                                                                                                                                                                                                                                                                                                          
                                                                                                                                               132                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4ky0b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ky0 B  10 LDYPVLWKILWGLVLGAVFGLIAGHFGYAGAVKTYIKPFGDLFVRLLKMLVMPIVLASLVVGAASISPARLGRVGVKIVVYYLATSAMAVFFGLIVGRLFNVGANVNLGSGTPPSLVQTLLNIVPTNPFASLAKGEVLPVIFFAIILGIAITYLMNRNEERVRKSAETLLRVFDGLAEAMYLIVGGVMQYAPIGVFALIAYVMAEQGVRVVGPLAKVVGAVYTGLFLQIVITYFILLKVFGIDPIKFIRKAKDAMITAFVTRSSSGTLPVTMRVAEEEMGVDKGIFSFTLPLGATINMDGTALYQGVTVLFVANAIGHPLTLGQQLVVVLTAVLASIGTAGVPGAGAIMLAMVLQSVGLDLTPGSPVALAYAMILGIDAILDMGRTMVNVTGDLAGTVIVAKTEKELDESKWI 429
                                    19        29        39        49        59        69        79        89        99       109       119 ||    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   
                                                                                                                                         121|                                                                                                                                                                                                                                                                                                            
                                                                                                                                          129                                                                                                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:422
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4ky0c_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ky0 C  10 LDYPVLWKILWGLVLGAVFGLIAGHFGYAGAVKTYIKPFGDLFVRLLKMLVMPIVLASLVVGAASISPARLGRVGVKIVVYYLATSAMAVFFGLIVGRLFNVGANVNLGSGTGKAIEAQPPSLVQTLLNIVPTNPFASLAKGEVLPVIFFAIILGIAITYLMNRNEERVRKSAETLLRVFDGLAEAMYLIVGGVMQYAPIGVFALIAYVMAEQGVRVVGPLAKVVGAVYTGLFLQIVITYFILLKVFGIDPIKFIRKAKDAMITAFVTRSSSGTLPVTMRVAEEEMGVDKGIFSFTLPLGATINMDGTALYQGVTVLFVANAIGHPLTLGQQLVVVLTAVLASIGTAGVPGAGAIMLAMVLQSVGLDLTPGSPVALAYAMILGIDAILDMGRTMVNVTGDLAGTVIVAKTEKELDESKWISH 431
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KY0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KY0)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Gly A:122 - Lys A:123   [ RasMol ]  
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