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(-) Description

Title :  PGLK FLIPPASE IN COMPLEX WITH INHIBITORY NANOBODY
 
Authors :  C. Perez, E. Pardon, J. Steyaert, K. P. Locher
Date :  01 Mar 17  (Deposition) - 03 May 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Abc Transporter Flippase, Nanobody, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Perez, M. Kohler, D. Janser, E. Pardon, J. Steyaert, R. Zenobi, K. P. Locher
Structural Basis Of Inhibition Of Lipid-Linked Oligosaccharide Flippase Pglk By A Conformational Nanobody.
Sci Rep V. 7 46641 2017
PubMed-ID: 28422165  |  Reference-DOI: 10.1038/SREP46641

(-) Compounds

Molecule 1 - WLAB PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: WLAB
    Mutation: YES
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 197
 
Molecule 2 - NANOBODY
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:385 , GLY A:387 , SER A:389 , THR A:390binding site for residue ADP A 601
2AC2SOFTWARETHR B:125 , TYR B:358 , LYS B:361 , GLY B:385 , CYS B:386 , GLY B:387 , LYS B:388 , SER B:389 , THR B:390binding site for residue ADP B 601

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1C:22 -C:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5NBD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NBD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5NBD)

(-) Exons   (0, 0)

(no "Exon" information available for 5NBD)

(-) 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:564
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.................eee....................eee....eeee.....hhhhhhhhhh.................hhhhhhhhhhhee...........hhhhhhhh....hhhhhhhhhhhh.hhhhhh...hhhhh.........hhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhh....eeee............eeeee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5nbd A   1 MVKKLFFILSKEDKNFLFFLLVFSVFVSFIETFAISLVMPFITLASDFSYFDRNKYLISLKEYLNIPVFEIIVYFGVGLIVFYVFRALLNAYYFHLLARFSKGRKHAIAYKVFSKFLNINYEKFTQKNQSEILKSITGEVYNLSTMISSFLLLMSEIFVVLLLYALMLLINYKITLFLSIFMVLNAFILVKILSPIIKKAGLRREEAMKNFFEILNTNLNNFKFIKLKTKEDGVLSLFKAQSEAFSKANITNESVAAVPRIYLEGIGFCVLVFIVVFLVLKNESDISGILSTISIFVLALYRLMPSANRIITSYHDLLYYHSSLNIIYQNLRQEEENLGEGKLSFNQELKICNLSFGYEGKKYLFKNLNLNIKKGEKIAFIGESGCGKSTLVDLIIGLLKPKEGQILIDKQELNASNAKNYRQKIGYIPQNIYLFNDSIAKNITFGDAVDEEKLNKVIKQANLEHFIKNLPQGVQTKVGDGGSNLSGGQKQRIAIARALYLEPEILVLDQATSALDTQSEAKIMDEIYKISKDKTMIIIAHRLSTITQCDKVYRLEHGKLKEEK 564
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Chain B from PDB  Type:PROTEIN  Length:564
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............................................eeee.....hhhhhhhhhh.................hhhhhhhhh..ee...........hhhhhhhh........hhhhhhhh.hhhhhh...hhhhh.........hhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhh...eeee..............eee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5nbd B   1 MVKKLFFILSKEDKNFLFFLLVFSVFVSFIETFAISLVMPFITLASDFSYFDRNKYLISLKEYLNIPVFEIIVYFGVGLIVFYVFRALLNAYYFHLLARFSKGRKHAIAYKVFSKFLNINYEKFTQKNQSEILKSITGEVYNLSTMISSFLLLMSEIFVVLLLYALMLLINYKITLFLSIFMVLNAFILVKILSPIIKKAGLRREEAMKNFFEILNTNLNNFKFIKLKTKEDGVLSLFKAQSEAFSKANITNESVAAVPRIYLEGIGFCVLVFIVVFLVLKNESDISGILSTISIFVLALYRLMPSANRIITSYHDLLYYHSSLNIIYQNLRQEEENLGEGKLSFNQELKICNLSFGYEGKKYLFKNLNLNIKKGEKIAFIGESGCGKSTLVDLIIGLLKPKEGQILIDKQELNASNAKNYRQKIGYIPQNIYLFNDSIAKNITFGDAVDEEKLNKVIKQANLEHFIKNLPQGVQTKVGDGGSNLSGGQKQRIAIARALYLEPEILVLDQATSALDTQSEAKIMDEIYKISKDKTMIIIAHRLSTITQCDKVYRLEHGKLKEEK 564
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560    


Chain C from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..........eeeeeee..........eeeee.......eeeeee......ee.hhhhh......ee....eeeeeee....................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nbd C   1 QVQLQESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAITSGGGSTSYSDAVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAKGYVVDFLDLAEYDSWGQGTQVTVSS 123
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
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  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 5NBD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5NBD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5NBD)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        O86150_CAMJU | O86150: 5c73 5c76 5c78

(-) Related Entries Specified in the PDB File

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