Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF APO MEND FROM M. TUBERCULOSIS - I222
 
Authors :  J. M. Johnston, E. N. M. Jirgis, G. Bashiri, E. M. M. Bulloch, E. N. Baker
Date :  16 Nov 15  (Deposition) - 22 Jun 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Menaquinone Biosynthesis, Mend, 2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3- Cyclohexadiene-1-Carboxylate Synthase, Thiamin-Diphosphate Dependent Enzyme, Pyruvate Oxidase Family, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. N. Jirgis, G. Bashiri, E. M. Bulloch, J. M. Johnston, E. N. Baker
Structural Views Along The Mycobacterium Tuberculosis Mend Reaction Pathway Illuminate Key Aspects Of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Structure V. 24 1167 2016
PubMed-ID: 27291649  |  Reference-DOI: 10.1016/J.STR.2016.04.018

(-) Compounds

Molecule 1 - 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE-1- CARBOXYLATE SYNTHASE
    Chains: A
    EC Number: 2.2.1.9
    Engineered: YES
    Expression System: MYCOBACTERIUM SMEGMATIS
    Expression System Taxid: 1772
    Gene: MEND, RV0555
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Other Details: THE PROTEIN WAS EXPRESSED AS A HIS-TAG CONSTRUCT AND CONTAINS A N-TERMINAL POLY-HISTIDINE TAG SEQUENCE NOT SEEN IN THE CRYSTAL STRUCTURE. THE PROTEIN HAS BEEN NUMBERED AS IT WOULD BE IN THE NON-TAGGED PROTEIN SO AS TO MATCH THE DEPOSITED BIOLOGICAL SEQUENCE (E.G. START 1 = RESIDUE 1 IN SEQUENCE DATABASE).
    Strain: ATCC 25618 / H37RV
    Synonym: SEPHCHC SYNTHASE,MENAQUINONE BIOSYNTHESIS PROTEIN MEND

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5ERX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERX)

(-) 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:508
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh..eeeee...hhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhhh........eeee.......hhhhh............eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhh.....eeee............eeeee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhh..........eeeeeee.....hhhhhhh......hhhhhhhhh..eeee.hhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5erx A   2 NPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSANYFGTQVRASISLGLAEDAPERTSALNATWRSATCRVLAAATGARTANAGPVHFDIPLTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGGGDVSSRIFGTPHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL 554
                                    11        21        31        41        51        61        71        81        91       101    || 129       139       149       159       169       179 ||    203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473|      496       506       516       526       536       546        
                                                                                                                                  106|                                                     181|                                                                                                                                                                                                                                                                                  473|                                                                   
                                                                                                                                   125                                                      196                                                                                                                                                                                                                                                                                   487
   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 5ERX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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 5erx)
 
  Sites
(no "Sites" information available for 5erx)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5erx)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  5erx
    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
  MEND_MYCTU | P9WK11
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.2.1.9
    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
  MEND_MYCTU | P9WK11
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MEND_MYCTU | P9WK11: 5ery 5esd 5eso 5ess 5esu

(-) Related Entries Specified in the PDB File

5ery 5esd 5eso 5ess 5esu