Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  MYCOBACTERIUM SMEGMATIS MBTA APO STRUCTURE
 
Authors :  L. Favrot, O. Vergnolle, J. S. Blanchard
Date :  09 Jun 16  (Deposition) - 14 Sep 16  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym./Biol. Unit :  A
Keywords :  2, 3-Dihydroxybenzoate-Amp Ligase, Mycobactin, Acetyl-Coa Synthetase- Like, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Vergnolle, H. Xu, J. M. Tufariello, L. Favrot, A. A. Malek, W. R. Jacobs, J. S. Blanchard
Post-Translational Acetylation Of Mbta Modulates Mycobacterial Siderophore Biosynthesis.
J. Biol. Chem. V. 291 22315 2016
PubMed-ID: 27566542  |  Reference-DOI: 10.1074/JBC.M116.744532

(-) Compounds

Molecule 1 - 2,3-DIHYDROXYBENZOATE-AMP LIGASE
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MBTA, MSMEG_4516, MSMEI_4404
    Organism Scientific: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / MC(2)155)
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5KEI)

(-) Sites  (0, 0)

(no "Site" information available for 5KEI)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KEI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:217 -Gly A:218
2Cys A:263 -Pro A:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KEI)

(-) 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:527
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhh........hhhhhhhhhhh...eeee....eeehhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeeee...hhhhhhhhhhh....eeeee......eehhhhhh...............eeeeee.........eeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh..eeeehhhhhhhhhh......eeee.....hhhhhhhhhhhh...eeeeee.....eee.....hhhhhhhh..ee.....eeeee............eeeeee..........hhhhhhhhh.....eeeeeeeee.........eeeeee...eeee..eeeehhhhhhhhhh...eeeeeeeeeee...eeeeeeeeee.....hhhhhhhhhhhh..hhhhh..eeee............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kei A  18 QSSLLAGFTPFPAERAQAYRAAGYWRDQLLDSVLRTAARTWPDHIAVIDADHRHTYAELDRLADRAAAGIAGLGIRPGDRVLVQLPNTAEFAVALFGLLRAGAVPVMCLPGHRLAELTHFAEVSSAVALVVADTHRDLARELVRSHPDVRHVLVDGDAAEFLSWAEVTRAAPGPVPEIAPDPAAPALLLVSGGTTGAPKLIPRTHQDYVYNATASAELCRLTADDVYLVALPAAHNFPLACPGLLGAMTVGATTVFTTDPSPEAAFAAIDEHGVTATALVPALAKLWAQACKTLRLLQVGGAKLAAPDAALVRGALTPGLQQVFGMAEGLLNYTRIGDPPEVLENTQGRPLSPDDEIRIVDEVGNEVPPGAEGELLVRGPYTLNGYFNAEAANERSFSPDGFYRSGDRVRRFADGPLAGYLEVTGRIKDVIVRGGENVSALDLEEHLLTHPSVWAAAAVALPDEFLGEKICAVVVFNGPPVSLAELHAHLEQRGVAAHSRPDALVPMPSLPTTAVGKIDKKAIVRQL 556
                                    27        37        47        57        67        77        87        97       107       117       127       137       147   ||  162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312||     329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       
                                                                                                                                                               151|                                                                                                                                                         313|                                                                                                                                                                                                                                           
                                                                                                                                                                157                                                                                                                                                          321
   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 5KEI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5kei)
 
  Sites
(no "Sites" information available for 5kei)
 
  Cis Peptide Bonds
    Cys A:263 - Pro A:264   [ RasMol ]  
    Thr A:217 - Gly A:218   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5kei
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A0R0V0_MYCS2 | A0R0V0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A0R0V0_MYCS2 | A0R0V0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5KEI)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KEI)