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 A PUTATIVE 4-HYDROXYPROLINE EPIMERASE/3-HYDROXYPROLINE DEHYDRATSE FROM THE SOIL BACTERIUM OCHROBACTERIUM ANTHROPI, TARGET EFI-506495, DISORDERED LOOPS
 
Authors :  M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wa S. Sojitra, M Stead, E. Washington, A. Scott Glen, S. Chowdhury, B. E J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerl S. C. Almo, Enzyme Function Initiative (Efi)
Date :  18 Apr 13  (Deposition) - 01 May 13  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Proline Racemase, Proposed 3-Oh Proline Dehydratase, Efi, Enzyme Function Intiative, Structural Genomics, Enzyme Function Initiative, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, M. Stead, E. Washington, A. Scott Glen, S. Chowdhury, B. Evens, J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of A Putative 4-Hydroxyproline Epimerase/3-Hydroxyproline Dehydratse From The Soil Bacterium Ochrobacterium Anthropi, Target Efi-506495, Disordered Loops
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROLINE RACEMASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OANT_0439
    Organism Scientific: OCHROBACTRUM ANTHROPI
    Organism Taxid: 439375
    Strain: ATCC 49188

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4K8L)

(-) Sites  (0, 0)

(no "Site" information available for 4K8L)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:259 -A:290

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:54 -Pro A:55
2Glu A:111 -Pro A:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K8L)

(-) Exons   (0, 0)

(no "Exon" information available for 4K8L)

(-) 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4k8la_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee..ee.eeeee........hhhhhhhhhhhhhhhhhhhhh.........eeeee........eeeeee........hhhhhhhhhhhhhhh........eeeeeeee..eeeeeeeeee..eeeeeeee....eeeeeeeee....eeeeeee...eeeeee.......hhhhhhhhhhhhhhhh.............eeeee...eee..eee..eeee..hhhhhhhhhhhhhh.......eee..eeeeeeeee..eeeeeeeeee.eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k8l A   0 SMRSTKVIHIVGCHAEGEVGDVIVGGVAPPPGKTVWEQSRFIASDETLRNFVLNEPRGGVFRHVNLLVPPKDPRAQMGFIIMEPADTPPMSGSNSICVSTVLLDSGIIPMQEPVTRMVLEAPGGLIEVEAECRNGKAERISVRNVPSFADRLNASLEVGTITVDTAYGGDSFVIVDAASIGMELAEIGVKITKAANEQLGFRHPEKDWNHISFCQITEPVTRDGDILTGVNTVAITGTGCSARMAVLHAKGQMKVGERFIGHCRLDKTLELGGKPAISPIISGRAWVTGTSQLMLDPSDPFPSGY 332
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       162       172       182 ||    200       210       220       230       240    || 259       269       279||     297       307       317       327     
                                                                                                                                                                                       157|                    184|                                                 245|                      280|                                           
                                                                                                                                                                                        161                     193                                                  255                       289
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K8L)

(-) Gene Ontology  (2, 2)

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 4k8l)
 
  Sites
(no "Sites" information available for 4k8l)
 
  Cis Peptide Bonds
    Glu A:111 - Pro A:112   [ RasMol ]  
    Glu A:54 - Pro A:55   [ 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
  4k8l
    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
  4HPE1_OCHA4 | A6WW16
    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
  4HPE1_OCHA4 | A6WW16
    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 4K8L)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4K8L)