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 SCYLLO-INOSITOL DEHYDROGENASE FROM LACTOBACILLUS CASEI
 
Authors :  D. Bertwistle, V. Linda, D. A. R. Sanders, D. R. J. Palmer
Date :  05 Sep 13  (Deposition) - 04 Mar 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Nad, Sugar Alcohol Dehydrogenases, Rossmann Fold, Dehydrogenase, Scyllo-Inositol, Dehydrogenate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Bertwistle, H. Aamudalapalli, L. Vogt, D. A. R. Sanders, D. R. J. Palmer
Crystal Structure Of Apo Scyllo-Inositol Dehydrogenase From Lactobacillus Casei
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INOSITOL DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-80L
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IDH, IOLG, IOLG2, LCABL_02220
    Organism Scientific: LACTOBACILLUS CASEI
    Organism Taxid: 543734
    Strain: BL23
    Synonym: SCYLLO-INOSITOL DEHYDROGENASE

 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 4MKX)

(-) Sites  (0, 0)

(no "Site" information available for 4MKX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MKX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:99 -Pro A:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MKX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MKX)

(-) Exons   (0, 0)

(no "Exon" information available for 4MKX)

(-) 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh..eee.hhhhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee..hhhhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhh.....eeeeeeee....eeeeeeeeee....eeeeeeee...eeee..........eee..eee.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mkx A   1 MTQKTIKIGIVGLGRLGKIHATNIATKIQHAKLQAATSVVPAELDWAKKELGVEEVFEDFDDMVQHADIDAVFIVSPSGFHLQQIESALNAGKHVFSEKPIGLDIEAIEHTQQVIAQHANLKFQLGFMRRFDDSYRYAKQLVDQGKIGDITLIRSYSIDPAAGMASFVKFSGGLFLDMSIHDIDVIRWFTGKEIDKVWAIGLNRAYPVLDKAGELETGAALMQLEDKTMAILVAGRNAAHGYHVETEIIGTKGMLRIAQVPEKNLVTVMNEEGIIRPTSQNFPERFAQAFLSEEQAFVNSILNNQDVGITAEDGLQGTKAALALQEAFEKNDIVQVAS 343
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170|      185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335        
                                                                                                                                                                                                   170|                                                                                                                                                                       
                                                                                                                                                                                                    176
   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 4MKX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MKX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MKX)

(-) Gene Ontology  (3, 3)

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 4mkx)
 
  Sites
(no "Sites" information available for 4mkx)
 
  Cis Peptide Bonds
    Lys A:99 - Pro A:100   [ RasMol ]  
 
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
  4mkx
    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
  A5YBJ8_LACCA | A5YBJ8
    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)
  1.1.1.-
    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
  A5YBJ8_LACCA | A5YBJ8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A5YBJ8_LACCA | A5YBJ8: 4mkz

(-) Related Entries Specified in the PDB File

3cea 3mz0 3nt4 3ntq 4mie 4min 4mio 4miy 4mjl 4mkz