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

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF E. COLI YBDB COMPLEXED WITH 2,4-DIHYDROXYPHENACYL-COA
 
Authors :  W. Ru, J. D. Farelli, D. Dunaway-Mariano, K. N. Allen
Date :  12 Apr 13  (Deposition) - 30 Jul 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hotdog Fold, Thioeatsrase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, J. A. Latham, D. Chen, J. Farelli, H. Zhao, K. Matthews, K. N. Allen, D. Dunaway-Mariano
Structure And Catalysis In The Escherichia Coli Hotdog-Fold Thioesterase Paralogs Ydii And Ybdb.
Biochemistry V. 53 4788 2014
PubMed-ID: 25010423  |  Reference-DOI: 10.1021/BI500334V

(-) Compounds

Molecule 1 - PROOFREADING THIOESTERASE ENTH
    Chains: A, B
    EC Number: 3.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-23A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B0597, ENTH, JW0589, YBDB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: ENTEROBACTIN SYNTHASE COMPONENT H, P15

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2HFQ2Ligand/Ion2,4-DIHYDROXYPHENACYL COENZYME A
3MLI1Ligand/IonMALONATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:48 , LEU A:53 , HIS A:54 , GLY A:55 , ASP A:76 , HIS A:89 , HIS A:90 , ARG A:91 , PRO A:92 , THR B:64 , SER B:67 , MET B:68 , VAL B:81 , GLY B:82 , THR B:83 , HIS B:106 , GLY B:108 , ARG B:109 , GLN B:110 , ASN B:111 , LEU B:136 , ACT B:203BINDING SITE FOR RESIDUE HFQ A 201
2AC2SOFTWAREASP A:10 , HOH A:321 , HOH A:328 , GLY B:123 , ARG B:124 , ARG B:125BINDING SITE FOR RESIDUE MLI A 202
3AC3SOFTWARETHR A:64 , SER A:67 , VAL A:81 , GLY A:82 , GLY A:108 , ARG A:109 , GLN A:110 , ASN A:111 , LEU A:136 , GLN B:48 , PRO B:49 , LEU B:53 , HIS B:54 , GLY B:55 , ARG B:75 , GLY B:77 , HIS B:89 , HIS B:90 , ARG B:91 , PRO B:92 , ACT B:202 , HOH B:312BINDING SITE FOR RESIDUE HFQ B 201
4AC4SOFTWAREPHE A:71 , PRO B:49 , PHE B:50 , HFQ B:201BINDING SITE FOR RESIDUE ACT B 202
5AC5SOFTWAREPRO A:49 , HFQ A:201 , THR B:15 , MET B:68 , PHE B:71BINDING SITE FOR RESIDUE ACT B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K4D)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:136 -Gly A:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K4D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K4D)

(-) Exons   (0, 0)

(no "Exon" information available for 4K4D)

(-) 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:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4d A   1 MIWKRHLTLDELNATSDNTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMMTRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVLG 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain B from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4d B   1 MIWKRHLTLDELNATSDNTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMMTRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVLG 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 4K4D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K4D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K4D)

(-) Gene Ontology  (9, 9)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HFQ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:136 - Gly A:137   [ 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 | Asym./Biol. Unit - 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
  4k4d
    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
  ENTH_ECOLI | P0A8Y8
    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)
  3.1.2.-
    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
  ENTH_ECOLI | P0A8Y8
    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
        ENTH_ECOLI | P0A8Y8: 1vh9 4k4c

(-) Related Entries Specified in the PDB File

1vh9 4k49 4k4a 4k4b 4k4c