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

(-) Description

Title :  CRYSTAL STRUCTURE OF DMDD E121A IN COMPLEX WITH MTA-COA
 
Authors :  D. Tan, L. Tong
Date :  29 Jan 13  (Deposition) - 05 Jun 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Enoyl-Coa Hydratase, Hydrolase, Methylthioacryloyl-Coa (Mta-Coa), Dimethyl-Sulphoniopropionate (Dmsp) Metabolism, Crotonase Fold, Enyol-Coa Hydratase, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex, Hydrolase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Tan, W. M. Crabb, W. B. Whitman, L. Tong
Crystal Structure Of Dmdd, A Crotonase Superfamily Enzyme That Catalyzes The Hydration And Hydrolysis Of Methylthioacryloyl-Coa.
Plos One V. 8 63870 2013
PubMed-ID: 23704947  |  Reference-DOI: 10.1371/JOURNAL.PONE.0063870

(-) Compounds

Molecule 1 - ENOYL-COA HYDRATASE/ISOMERASE FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 26B
    Expression System Strain: BL-21 STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DMDD
    Mutation: YES
    Organism Scientific: RUEGERIA POMEROYI
    Organism Taxid: 246200
    Strain: DSS-3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
11GZ2Ligand/IonMETHYLTHIOACRYLOYL-COA
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
11GZ6Ligand/IonMETHYLTHIOACRYLOYL-COA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:30 , LYS A:31 , ARG A:32 , ALA A:34 , ALA A:69 , GLY A:70 , LEU A:71 , ASP A:72 , LEU A:73 , VAL A:74 , VAL A:116 , GLY A:117 , GLY A:118 , TYR A:136 , PRO A:140 , GLU A:141 , GLY A:149 , HOH A:460 , HOH A:489 , HOH A:547 , HOH A:569 , HOH A:618 , HOH A:647 , HOH A:653 , LYS B:53 , HOH B:511 , HOH B:563BINDING SITE FOR RESIDUE 1GZ A 301
2AC2SOFTWAREASP B:30 , LYS B:31 , ARG B:32 , ALA B:34 , HIS B:66 , ALA B:69 , LEU B:71 , ASP B:72 , LEU B:73 , GLY B:118 , TYR B:136 , PRO B:140 , ARG B:144 , GLY B:149 , PHE B:255 , LYS B:258 , ARG B:262 , VAL B:263 , ARG B:264 , HOH B:467 , HOH B:539 , HOH B:558 , HOH B:562BINDING SITE FOR RESIDUE 1GZ B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IZC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IZC)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains d4izca_ A: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeee...eeehhhhhhhhh..eeee....eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhh...ee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izc A   3 QDVTSGYSNLDLDLRDNGVCVVTLNRPDKRNALDVATIEELVTFFSTAHRKGVRAVVLTGAGDHFCAGLDLVEHWKADRSADDFMHVCLRWHEAFNKMEYGGVPIIAALRGAVVGGGLALASAAHLRVMDQSTYFALPEGQRGIFTGGGATIRVSDMIGKYRMIDMILTGRVYQGQEAADLGLAQYITEGSSFDKAMELADKIASNLPLTNFAICSAISHMQNMSGLDAAYAEAFVGGIVNTQPAARERLE 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252 


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains d4izcb_ B: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeee...eeehhhhhhhhh..eeee....eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhh...ee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izc B   2 TQDVTSGYSNLDLDLRDNGVCVVTLNRPDKRNALDVATIEELVTFFSTAHRKGVRAVVLTGAGDHFCAGLDLVEHWKADRSADDFMHVCLRWHEAFNKMEYGGVPIIAALRGAVVGGGLALASAAHLRVMDQSTYFALPEGQRGIFTGGGATIRVSDMIGKYRMIDMILTGRVYQGQEAADLGLAQYITEGSSFDKAMELADKIASNLPLTNFAICSAISHMQNMSGLDAAYAEAFVGGIVNTQPAARERLEAFANKTAARVRPNS 267
                                    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
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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
    1GZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4izc)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  4izc
    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
  DMDD_RUEPO | Q5LLW6
    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)
  (no 'Enzyme Classificator' available)
    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
  DMDD_RUEPO | Q5LLW6
    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
        DMDD_RUEPO | Q5LLW6: 4izb 4izd

(-) Related Entries Specified in the PDB File

4izb CRYSTAL STRUCTURE OF DMDD FREE ENZYME.
4izd