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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL EXTRACELLULAR DOMAIN OF MYCOBACTERIUM TUBERCULOSIS EMBC
 
Authors :  L. J. Alderwick, G. S. Besra, K. Futterer
Date :  03 Dec 10  (Deposition) - 15 Dec 10  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Beta-Sandwich, Carbohydrate Binding, Carbohydrate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Alderwick, G. S. Lloyd, H. Ghadbane, J. W. May, A. Bhatt, L. Eggeling, K. Futterer, G. S. Besra
The C-Terminal Domain Of The Arabinosyltransferase Mycobacterium Tuberculosis Embc Is A Lectin-Like Carbohydrate Binding Module.
Plos Pathog. V. 7 E1001 2011
PubMed-ID: 21383969  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1001299

(-) Compounds

Molecule 1 - ARABINOSYLTRANSFERASE C
    ChainsA
    EC Number2.4.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23B
    Expression System StrainC41(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN (UNP RESIDUES 719-1094)
    GeneEMBC, MT3900, MTCY13D12.27, RV3793
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    SynonymARABINOSYLTRANSFERASE EMBC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1AFO1Ligand/IonOCTYL ALPHA-D-ARABINOFURANOSIDE
2CA1Ligand/IonCALCIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1AFO2Ligand/IonOCTYL ALPHA-D-ARABINOFURANOSIDE
2CA-1Ligand/IonCALCIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:91 , GLY A:737 , ASN A:740 , TRP A:985 , GLY A:988 , LEU A:989 , ASP A:1051 , ARG A:1055BINDING SITE FOR RESIDUE AFO A 1
2AC2SOFTWAREHOH A:33 , HOH A:39 , HOH A:67 , ASP A:949 , ASP A:951 , HIS A:956BINDING SITE FOR RESIDUE CA A 1125
3AC3SOFTWAREASP A:793 , ARG A:890 , PRO A:924 , TRP A:957BINDING SITE FOR RESIDUE PO4 A 2

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:749 -A:993

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:923 -Pro A:924
2Ile A:1035 -Thr A:1036

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_EMBC_MYCTU_002 *R738QEMBC_MYCTU  ---  ---AR738Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_EMBC_MYCTU_002 *R738QEMBC_MYCTU  ---  ---AR738Q
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PTY)

(-) 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:284
 aligned with EMBC_MYCTO | P9WNL4 from UniProtKB/Swiss-Prot  Length:1094

    Alignment length:333
                                   744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064   
          EMBC_MYCTO    735 SVGRSNLQALAGKTCGLAEDVLVELDPNAGMLAPVTAPLADALGAGLSEAFTPNGIPADVTADPVMERPGDRSFLNDDGLITGSEPGTEGGTTAAPGINGSRARLPYNLDPARTPVLGSWRAGVQVPAMLRSGWYRLPTNEQRDRAPLLVVTAAGRFDSREVRLQWATDEQAAAGHHGGSMEFADVGAAPAWRNLRAPLSAIPSTATQVRLVADDQDLAPQHWIALTPPRIPRVRTLQNVVGAADPLFLDWLVGLAFPCQRPFGHQYGVDETPKWRILPDRFGAEANSPVMDHNGGGPLGITELLMRATTVASYLKDDWFRDWGALQRLTPYY 1067
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Arabinose_trans-3ptyA01 A:735-1067                                                                                                                                                                                                                                                                                                            Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhh.eeee.hhhhhh......hhhhhh...eee...........------------------------------...................hhhhh..ee.........eeee...ee...........eeeeeeee..hhh.eeeeeehhhhhhh....eeee.eee......eeeeee.hhh.....eeeeeeee........eee........eehhhhhh...eee.hhhhhh.....ee..hhhhh.....eeee...-------------------.....eeeeeeeeee.........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3pty A  735 SVGRSNLQALAGKTCGLAEDVLVELDPNAGMLAPVTAPLADALGAGLSEAFTPNGIPADV------------------------------GTTAAPGINGSRARLPYNLDPARTPVLGSWRAGVQVPAMLRSGWYRLPTNEQRDRAPLLVVTAAGRFDSREVRLQWATDEQAAAGHHGGSMEFADVGAAPAWRNLRAPLSAIPSTATQVRLVADDQDLAPQHWIALTPPRIPRVRTLQNVVGAADPVFLDWLVGLAFPCQRPFGHQYGVDETPKWRILPDR-------------------ITELLMRATTVASYLKDDWFRDWGALQRLTPYY 1067
                                   744       754       764       774       784       794         -         -         -|      834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014|        -         -|     1044      1054      1064   
                                                                                     794                            825                                                                                                                                                                                          1015                1035                                

Chain A from PDB  Type:PROTEIN  Length:284
 aligned with EMBC_MYCTU | P9WNL5 from UniProtKB/Swiss-Prot  Length:1094

    Alignment length:333
                                   744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064   
          EMBC_MYCTU    735 SVGRSNLQALAGKTCGLAEDVLVELDPNAGMLAPVTAPLADALGAGLSEAFTPNGIPADVTADPVMERPGDRSFLNDDGLITGSEPGTEGGTTAAPGINGSRARLPYNLDPARTPVLGSWRAGVQVPAMLRSGWYRLPTNEQRDRAPLLVVTAAGRFDSREVRLQWATDEQAAAGHHGGSMEFADVGAAPAWRNLRAPLSAIPSTATQVRLVADDQDLAPQHWIALTPPRIPRVRTLQNVVGAADPVFLDWLVGLAFPCQRPFGHQYGVDETPKWRILPDRFGAEANSPVMDHNGGGPLGITELLMRATTVASYLKDDWFRDWGALQRLTPYY 1067
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Arabinose_trans-3ptyA01 A:735-1067                                                                                                                                                                                                                                                                                                            Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhh.eeee.hhhhhh......hhhhhh...eee...........------------------------------...................hhhhh..ee.........eeee...ee...........eeeeeeee..hhh.eeeeeehhhhhhh....eeee.eee......eeeeee.hhh.....eeeeeeee........eee........eehhhhhh...eee.hhhhhh.....ee..hhhhh.....eeee...-------------------.....eeeeeeeeee.........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3pty A  735 SVGRSNLQALAGKTCGLAEDVLVELDPNAGMLAPVTAPLADALGAGLSEAFTPNGIPADV------------------------------GTTAAPGINGSRARLPYNLDPARTPVLGSWRAGVQVPAMLRSGWYRLPTNEQRDRAPLLVVTAAGRFDSREVRLQWATDEQAAAGHHGGSMEFADVGAAPAWRNLRAPLSAIPSTATQVRLVADDQDLAPQHWIALTPPRIPRVRTLQNVVGAADPVFLDWLVGLAFPCQRPFGHQYGVDETPKWRILPDR-------------------ITELLMRATTVASYLKDDWFRDWGALQRLTPYY 1067
                                   744       754       764       774       784       794         -         -         -|      834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014|        -         -|     1044      1054      1064   
                                                                                     794                            825                                                                                                                                                                                          1015                1035                                

   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 3PTY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: GT-C (2)

(-) Gene Ontology  (12, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (EMBC_MYCTO | P9WNL4)
molecular function
    GO:0052636    arabinosyltransferase activity    Catalysis of the transfer of an arabinosyl group from one compound (donor) to another (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0071766    Actinobacterium-type cell wall biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Actinobacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane. Actinobacterial cell walls contain characteristic mycolic acids, of which some are covalently linked to the cell wall peptidoglycan and others accumulate at the cell surface.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (EMBC_MYCTU | P9WNL5)
molecular function
    GO:0052636    arabinosyltransferase activity    Catalysis of the transfer of an arabinosyl group from one compound (donor) to another (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0071766    Actinobacterium-type cell wall biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Actinobacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane. Actinobacterial cell walls contain characteristic mycolic acids, of which some are covalently linked to the cell wall peptidoglycan and others accumulate at the cell surface.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009247    glycolipid biosynthetic process    The chemical reactions and pathways resulting in the formation of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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