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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALCANIVORAX BORKUMENSIS YDAH TRANSPORTER REVEALS AN UNUSUAL TOPOLOGY
 
Authors :  C. -C. Su, J. R. Bolla, E. W. Yu
Date :  30 Jul 14  (Deposition) - 29 Apr 15  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.96
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transmembrane Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Bolla, C. C. Su, J. A. Delmar, A. Radhakrishnan, N. Kumar, T. H. Chou, F. Long, K. R. Rajashankar, E. W. Yu
Crystal Structure Of The Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology.
Nat Commun V. 6 6874 2015
PubMed-ID: 25892120  |  Reference-DOI: 10.1038/NCOMMS7874

(-) Compounds

Molecule 1 - ABGT PUTATIVE TRANSPORTER FAMILY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ABO_0881, YDAH
    Organism Scientific: ALCANIVORAX BORKUMENSIS SK2
    Organism Taxid: 393595
    Strain: SK2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1BOG4Ligand/IonB-OCTYLGLUCOSIDE
2LMT6Ligand/IonDODECYL-BETA-D-MALTOSIDE
3NA4Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:390 , GLY A:394 , ASP A:429 , ASN A:433 , HOH A:901BINDING SITE FOR RESIDUE NA A 801
02AC2SOFTWARESER A:105 , ARG A:112 , ILE A:248 , MET A:253BINDING SITE FOR RESIDUE LMT A 802
03AC3SOFTWARELEU A:287BINDING SITE FOR RESIDUE LMT A 804
04AC4SOFTWAREHIS A:249 , ARG A:251 , TRP A:255 , THR A:259 , VAL A:313 , SER A:314 , GLU D:53 , THR D:54BINDING SITE FOR RESIDUE LMT A 805
05AC5SOFTWAREVAL A:88 , VAL A:323BINDING SITE FOR RESIDUE LMT A 806
06AC6SOFTWAREASN B:390 , GLY B:394 , ASP B:429 , ASN B:433 , HOH B:901BINDING SITE FOR RESIDUE NA B 801
07AC7SOFTWAREASN C:390 , GLY C:394 , ASP C:429 , ASN C:433 , HOH C:901BINDING SITE FOR RESIDUE NA C 801
08AC8SOFTWAREARG C:112BINDING SITE FOR RESIDUE BOG C 802
09AC9SOFTWARELEU C:102 , LEU C:106 , SER C:108 , ARG C:112BINDING SITE FOR RESIDUE LMT C 803
10BC1SOFTWAREGLY C:257BINDING SITE FOR RESIDUE BOG C 804
11BC2SOFTWAREVAL C:88 , VAL C:297 , LEU C:301BINDING SITE FOR RESIDUE LMT C 805
12BC3SOFTWAREASN D:390 , GLY D:394 , LYS D:399 , ASP D:429 , ASN D:433 , HOH D:901BINDING SITE FOR RESIDUE NA D 801
13BC4SOFTWAREHIS C:293 , GLY C:294 , VAL C:297 , LEU C:301 , PHE D:70 , THR D:71 , THR D:72 , LEU D:73 , VAL D:74 , HOH D:911BINDING SITE FOR RESIDUE BOG D 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R0C)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:491 -Pro A:492
2His B:234 -Ala B:235
3Gly B:491 -Pro B:492
4Gly D:491 -Pro D:492

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R0C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R0C)

(-) Exons   (0, 0)

(no "Exon" information available for 4R0C)

(-) 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:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r0c A  17 RLPHPTLLFVWFCLLLLPLTAVLGALDVTATHPLTDETITAHSLLDADGLRYLFTTLVGNFTGFAPLGVVLVAMLGLGVAEQSGLLSVSLASLVRRSSGGALVFTVAFAGVLSSLTVDAGYVVLIPLAGLVFQLAGRPPIAGIATAFAAVSGGFSANLLVGPVDATLAGLSTEAAHIIDPDRTVAATGNYWFIIASTFLVTGLVTLITRTLTEPRLAHANTVADASVDAPQIHSRAMKWTGLTLAILLAGLALLVLPNDAPLRHPDTGSVLGSPFIHGLVVIVALIAGICGAVYGRVSGQFRNSGAVITAMEVTMASMAGYLVLMFFAAQFVAWFNYSQLGLLLAVKGAAWLGALTVPKVVLLLLFVVLTALINLMIGSASAKWSILAPVFIPMLMLLGISPEASQAAYRVGDSSTNIITPLMPYFVLVLGFARRYQPETGIGTLIALMLPYSLTLLLGWSVLLGVWIGFGWPLGP 492
                                    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      


Chain B from PDB  Type:PROTEIN  Length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..eee......eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r0c B  19 PHPTLLFVWFCLLLLPLTAVLGALDVTATHPLTDETITAHSLLDADGLRYLFTTLVGNFTGFAPLGVVLVAMLGLGVAEQSGLLSVSLASLVRLVFTVAFAGVLSSLTVDAGYVVLIPLAGLVFQLAGRPPIAGIATAFAAVSGGFSANLLVGPVDATLAGLSTEAAHIIDPDRTVAATGNYWFIIASTFLVTGLVTLITRTLTEPRLAHANTVADASVDAPQIHSRAMKWTGLTLAILLAGLALLVLPNDAPLRHPDTGSVLGSPFIHGLVVIVALIAGICGAVYGRVSGQFRNSGAVITAMEVTMASMAGYLVLMFFAAQFVAWFNYSQLGLLLAVKGAAWLGALTVPKVVLLLLFVVLTALINLMIGSASAKWSILAPVFIPMLMLLGISPEASQAAYRVGDSSTNIITPLMPYFVLVLGFARRYQPETGIGTLIALMLPYSLTLLLGWSVLLGVWIGFGWPLGP 492
                                    28        38        48        58        68        78        88        98       108  ||   124       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       434       444       454       464       474       484        
                                                                                                                      111|                                                                                                                                                                                                                                                                                                                                                                                      
                                                                                                                       118                                                                                                                                                                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:474
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..eee......eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r0c C  19 PHPTLLFVWFCLLLLPLTAVLGALDVTATHPLTDETITAHSLLDADGLRYLFTTLVGNFTGFAPLGVVLVAMLGLGVAEQSGLLSVSLASLVRRSSGGALVFTVAFAGVLSSLTVDAGYVVLIPLAGLVFQLAGRPPIAGIATAFAAVSGGFSANLLVGPVDATLAGLSTEAAHIIDPDRTVAATGNYWFIIASTFLVTGLVTLITRTLTEPRLAHANTVADASVDAPQIHSRAMKWTGLTLAILLAGLALLVLPNDAPLRHPDTGSVLGSPFIHGLVVIVALIAGICGAVYGRVSGQFRNSGAVITAMEVTMASMAGYLVLMFFAAQFVAWFNYSQLGLLLAVKGAAWLGALTVPKVVLLLLFVVLTALINLMIGSASAKWSILAPVFIPMLMLLGISPEASQAAYRVGDSSTNIITPLMPYFVLVLGFARRYQPETGIGTLIALMLPYSLTLLLGWSVLLGVWIGFGWPLGP 492
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488    


Chain D from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eee......eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r0c D  10 RLEQLGNRLPHPTLLFVWFCLLLLPLTAVLGALDVTATHPLTDETITAHSLLDADGLRYLFTTLVGNFTGFAPLGVVLVAMLGLGVAEQSGLLSVSLASLVRRSSGGALVFTVAFAGVLSSLTVDAGYVVLIPLAGLVFQLAGRPPIAGIATAFAAVSGGFSANLLVGPVDATLAGLSTEAAHIIDPDRTVAATGNYWFIIASTFLVTGLVTLITRTLTEPRLAHANTVADASVDAPQIHSRAMKWTGLTLAILLAGLALLVLPNDAPLRHPDTGSVLGSPFIHGLVVIVALIAGICGAVYGRVSGQFRNSGAVITAMEVTMASMAGYLVLMFFAAQFVAWFNYSQLGLLLAVKGAAWLGALTVPKVVLLLLFVVLTALINLMIGSASAKWSILAPVFIPMLMLLGISPEASQAAYRVGDSSTNIITPLMPYFVLVLGFARRYQPETGIGTLIALMLPYSLTLLLGWSVLLGVWIGFGWPLGP 492
                                    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       439       449       459       469       479       489
   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 4R0C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R0C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R0C)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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