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 PUTATIVE ENOYL-COA HYDRATASE/ISOMERASE FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444
 
Authors :  D. R. Cooper, P. J. Porebski, M. J. Domagalski, M. Ahmed, M. Stead, B. Hil R. Seidel, M. Zimmerman, J. B. Bonanno, S. C. Almo, W. Minor, New York Structural Genomics Research Consortium (Nysgrc)
Date :  29 Mar 13  (Deposition) - 29 May 13  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Crotonase/Enoyl-Coenzyme A (Coa) Hydratase Superfamily, Pfam Pf00378, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Cooper, P. J. Porebski, M. J. Domagalski, M. Ahmed, M. Stead, B. Hillerich, R. Seidel, M. Zimmerman, J. B. Bonanno, S. C. Almo, W. Minor, New York Structural Genomics Research Consortium (Nysgrc)
Crystal Structure Of Putative Enoyl-Coa Hydratase/Isomerase From Novosphingobium Aromaticivorans Dsm 12444
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENOYL-COA HYDRATASE/ISOMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC-HIS
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SARO_0518
    Organism Scientific: NOVOSPHINGOBIUM AROMATICIVORANS
    Organism Taxid: 279238
    Strain: DSM 12444

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (2, 48)
No.NameCountTypeFull Name
1MSE42Mod. Amino AcidSELENOMETHIONINE
2UNL6Ligand/IonUNKNOWN LIGAND

(-) Sites  (0, 0)

(no "Site" information available for 4JYJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JYJ)

(-) 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:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....eeeeee.hhhhh...hhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..eee.hhhhhhhhh.eeeee...eee..........hhhhhhhhhhhhhhhhhhhh...eeehhhhhhh....eeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jyj A   6 DGVRLEEGDAIDWIVFDRPQAANSFSATLLEQFSALVKDRQANGAPVLGIRGSGRGFSSGmDLGEYNATSGPTSDVLRLSSYVERWLDLWRHPKPVIVAVHGYCIGVAAQLASFADILVVAEDAmISEPTIPIGGGFIAPTWVSHVGSRHAKEFAFLPGNRIDGRmAAAWGWANCAVPASEVIACCESLAQRmKLmPPAVLAmKKRSINRAmEAAGFHAAASAIAESDALLHLEPEVTAIRNRLRTEDLKAVVGSYAGESSQEIFQRHGG 275
                                    15        25        35        45        55        65|       75        85        95       105       115       125    |  135       145       155       165     | 175       185       195  |  | 205  |    215 |     225       235       245       255       265       275
                                                                                       66-MSE                                                         130-MSE                                  171-MSE                    198-MSE     |      217-MSE                                                      
                                                                                                                                                                                                                             201-MSE  |                                                                   
                                                                                                                                                                                                                                    208-MSE                                                               


Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....eeeeee.hhhhh...hhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eee.hhhhhhhhh.eeeee...eee..........hhhhhhhhhhhhhhhhhhhh...eeehhhhhhh....eeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jyj B   7 GVRLEEGDAIDWIVFDRPQAANSFSATLLEQFSALVKDRQANGAPVLGIRGSGRGFSSGmDLGEYNATSGPTSDVLRLSSYVERWLDLWRHPKPVIVAVHGYCIGVAAQLASFADILVVAEDAmISEPTIPIGGGFIAPTWVSHVGSRHAKEFAFLPGNRIDGRmAAAWGWANCAVPASEVIACCESLAQRmKLmPPAVLAmKKRSINRAmEAAGFHAAASAIAESDALLHLEPEVTAIRNRLRTEDLKAVVGSYAGESSQEIFQRHG 274
                                    16        26        36        46        56        66        76        86        96       106       116       126   |   136       146       156       166    |  176       186       196 |  |  206 |     216|      226       236       246       256       266        
                                                                                      66-MSE                                                         130-MSE                                  171-MSE                    198-MSE     |      217-MSE                                                     
                                                                                                                                                                                                                            201-MSE  |                                                                  
                                                                                                                                                                                                                                   208-MSE
   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 4JYJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4jyj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jyj)
 
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
  4jyj
    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
  Q2GB08_NOVAD | Q2GB08
    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)
  (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
  Q2GB08_NOVAD | Q2GB08
    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 4JYJ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JYJ)