Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 PUTATIVE L-ALANINE-DL-GLUTAMATE EPIMERASE FROM BURKHOLDERIA XENOVORANS STRAIN LB400
 
Authors :  J. B. Bonanno, M. Dickey, K. T. Bain, B. Wu, V. Sridhar, J. Freeman, L. Smy S. Atwell, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Resear For Structural Genomics (Nysgxrc)
Date :  25 Jan 07  (Deposition) - 06 Feb 07  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Structural Genomics, Enolase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, M. Dickey, K. T. Bain, B. Wu, V. Sridhar, J. Freeman, L. Smyth, S. Atwell, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain Lb400
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE L-ALANINE-DL-GLUTAMATE EPIMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: BXENO_B1104, BXE_B1897
    Organism Scientific: BURKHOLDERIA XENOVORANS
    Organism Taxid: 266265
    Strain: LB400

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1SO416Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:127 , ASN A:130 , HIS A:131 , HOH A:806BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREASP A:141 , LEU A:142 , HIS A:167 , HOH A:544BINDING SITE FOR RESIDUE SO4 A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OO6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Cys A:124 -Pro A:125
2Gly A:136 -Pro A:137
3Val A:181 -Pro A:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OO6)

(-) Exons   (0, 0)

(no "Exon" information available for 2OO6)

(-) 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:393
 aligned with Q13PB7_PARXL | Q13PB7 from UniProtKB/TrEMBL  Length:399

    Alignment length:394
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390    
         Q13PB7_PARXL     1 MKVVSVDTLCCDAGWRNYHFVKLTTDEGIVGWSEFDEGFGSPGVTAVIEQLGKRLVGASVMEHERFFAEAYCLTRPATGGVVSEGIGAIENALLDAKAKTLNVPCYELLGGKLRDRVPVYWSHCPTWRINHPKFFGPPVTDLDGVKRTAEEARERQFRAIKTNIFIHDDGPLHAWRPGFAVPFQPALNVDRKVLRNLRAHLEALRDGAGPDVEILLDLNFNAKPEGYLKILRELADFDLFWVEIDSYSPQGLAYVRNHSPHPISSCETLFGIREFKPFFDANAVDVAIVDTIWNGVWQSMKIAAFADAHDINVAPHNFYGHLCTMINANFAAAVPNLRIMETDIDRLAWEDELFTHAPEYQNGELIIPDRPGWGTDPVEEAILAHPPKVMGGLL 394
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2oo6A01 A:1-102,A:375-385 Enolase-like, N-terminal domain                                             2oo6A02 A:103-374 Enolase superfamily                                                                                                                                                                                                                                           2oo6A01    --------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeee....eeeeee.......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......eeeeee...hhhhhhh.........hhhhhhhhhhhhhhh...eeee..ee......ee.hhhhh.........hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eee....hhhhhhhhhhh....eee....hhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh.....eee.......hhhhh....eee..eee...........hhhhhhhh....-.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oo6 A   1 LKVVSVDTLCCDAGWRNYHFVKLTTDEGIVGWSEFDEGFGSPGVTAVIEQLGKRLVGASVMEHERFFAEAYCLTRPATGGVVSEGIGAIENALLDAKAKTLNVPCYELLGGKLRDRVPVYWSHCPTWRINHPKFFGPPVTDLDGVKRTAEEARERQFRAIKTNIFIHDDGPLHAWRPGFAVPFQPALNVDRKVLRNLRAHLEALRDGAGPDVEILLDLNFNAKPEGYLKILRELADFDLFWVEIDSYSPQGLAYVRNHSPHPISSCETLFGIREFKPFFDANAVDVAIVDTIWNGVWQSMKIAAFADAHDINVAPHNFYGHLCTMINANFAAAVPNLRIMETDIDRLAWEDELFTHAPEYQNGELIIPDRPGWGTDPVEEAILAHPPKV-GGLL 394
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380        |-|   
                                                                                                                                                                                                                                                                                                                                                                                                                              389 |   
                                                                                                                                                                                                                                                                                                                                                                                                                                391
   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 2OO6)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OO6)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q13PB7_PARXL | Q13PB7)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:124 - Pro A:125   [ RasMol ]  
    Gly A:136 - Pro A:137   [ RasMol ]  
    Val A:181 - Pro A:182   [ 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 | 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
  2oo6
    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
  Q13PB7_PARXL | Q13PB7
    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
  Q13PB7_PARXL | Q13PB7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q13PB7_PARXL | Q13PB7: 3go2 3sn0 3sn1 3sn4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OO6)