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(-) Description

Title :  CLOSED LIGANDED CRYSTAL STRUCTURE OF XYLOSE BINDING PROTEIN FROM ESCHERICHIA COLI
 
Authors :  S. Sooriyaarachchi, W. Ubhayasekera, S. L. Mowbray
Date :  23 Mar 10  (Deposition) - 18 Aug 10  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Xylose Binding Protein, Xylose, Conformational Changes, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Sooriyaarachchi, W. Ubhayasekera, C. Park, S. L. Mowbray
Conformational Changes And Ligand Recognition Of Escherichi Coli D-Xylose Binding Protein Revealed
J. Mol. Biol. V. 402 657 2010
PubMed-ID: 20678502  |  Reference-DOI: 10.1016/J.JMB.2010.07.038

(-) Compounds

Molecule 1 - D-XYLOSE-BINDING PERIPLASMIC PROTEIN
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPEXP-5-CT/TOPO
    Expression System StrainBL21(AI)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid511145
    StrainK-12 SUBSTR. MG1655
    SynonymXYLOSE BINDING PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1XYP3Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1XYP1Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1XYP1Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:14 , ARG A:16 , ASP A:90 , ARG A:91 , ASP A:135 , ASN A:137 , TRP A:169 , ASN A:196 , ASP A:222 , LYS A:242BINDING SITE FOR RESIDUE XYP A 400
2AC2SOFTWARELEU B:14 , ARG B:16 , ASP B:90 , ARG B:91 , ASP B:135 , ASN B:137 , TRP B:169 , ASN B:196 , ASP B:222 , LYS B:242BINDING SITE FOR RESIDUE XYP B 401
3AC3SOFTWARELEU C:14 , ARG C:16 , ASP C:90 , ARG C:91 , ASP C:135 , ASN C:137 , TRP C:169 , ASN C:196 , ASP C:222 , LYS C:242BINDING SITE FOR RESIDUE XYP C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MA0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MA0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MA0)

(-) Exons   (0, 0)

(no "Exon" information available for 3MA0)

(-) Sequences/Alignments

Asymmetric 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:313
 aligned with XYLF_ECOLI | P37387 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:313
                                                                                                                                                                                                                                                                                                                                            330      
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      |  -   
           XYLF_ECOLI    24 KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh..eeeee..........eeeeehhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.......ee.....hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh.......eeee....eeeeeee..eeee..............hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ma0 A   1 KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESELHHHHHH 313
                                    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   

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with XYLF_ECOLI | P37387 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:306
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
           XYLF_ECOLI    25 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 330
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh..eeeee..........eeeeehhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh......ee.....hhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhh.......eeee....eeeeeee..eeehhhhh..........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ma0 B   2 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301      

Chain C from PDB  Type:PROTEIN  Length:306
 aligned with XYLF_ECOLI | P37387 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:306
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
           XYLF_ECOLI    25 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 330
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---Peripla_BP_4-3ma0C01 C:5-263                                                                                                                                                                                                                                       -------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Peripla_BP_4-3ma0C02 C:5-263                                                                                                                                                                                                                                       -------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---Peripla_BP_4-3ma0C03 C:5-263                                                                                                                                                                                                                                       -------------------------------------------- Pfam domains (3)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhh..eeeee..........eeeeehhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.......ee.....hhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhh.......eeee....eeeeeee..eee...hhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ma0 C   2 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301      

   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 3MA0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MA0)

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (XYLF_ECOLI | P37387)
molecular function
    GO:0048029    monosaccharide binding    Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
biological process
    GO:0015753    D-xylose transport    The directed movement of D-xylose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. D-xylose (the naturally occurring enantiomer is always D-) is a constituent of plant polysaccharides.
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        XYLF_ECOLI | P373873m9w 3m9x

(-) Related Entries Specified in the PDB File

3m9w OPEN LIGAND FREE XYLOSE BINDING PROTEIN STRUCTURE FROM ESCHERICHIA COLI
3m9x OPEN LIGANDED XYLOSE BINDING PROTEIN STRUCTURE FROM ESCHERICHIA COLI