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 PUTATIVE L-ALANINE-DL-GLUTAMATE EPIMERASE FROM BURKHOLDERIA XENOVORANS STRAIN LB400 BOUND TO MAGNESIUM AND FUMARATE
 
Authors :  J. B. Bonanno, Y. Patskovsky, R. Toro, M. Dickey, K. T. Bain, B. Wu, J. M. S S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  28 Jun 11  (Deposition) - 27 Jul 11  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Structural Genomics, Unknown Function, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, Y. Patskovsky, R. Toro, M. Dickey, K. T. Bain, B. Wu, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative L-Alanine-Dl-Glutamate Epimerase From Burkholderia Xenovorans Strain Lb400 Bound T Magnesium And Fumarate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE L-ALANINE-DL-GLUTAMATE EPIMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    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  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FUM1Ligand/IonFUMARIC ACID
3MG1Ligand/IonMAGNESIUM ION
4MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 48)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FUM8Ligand/IonFUMARIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4MSE40Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:217 , GLU A:243 , GLU A:267 , HOH A:634 , HOH A:647 , HOH A:694BINDING SITE FOR RESIDUE MG A 408
2AC2SOFTWAREHIS A:123 , LYS A:161 , ASN A:163 , ARG A:176 , PHE A:179 , ASP A:217 , ASN A:219 , LEU A:393 , HOH A:601 , HOH A:647 , HOH A:655 , HOH A:728 , HOH A:887BINDING SITE FOR RESIDUE FUM A 500
3AC3SOFTWAREARG A:114 , GLN A:184 , PRO A:185 , ALA A:186 , HOH A:876BINDING SITE FOR RESIDUE CL A 502
4AC4SOFTWAREARG A:16 , ASN A:17 , GLY A:38 , GLY A:391 , HOH A:726BINDING SITE FOR RESIDUE CL A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SN0)

(-) 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 3SN0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SN0)

(-) Exons   (0, 0)

(no "Exon" information available for 3SN0)

(-) 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:401
 aligned with Q13PB7_PARXL | Q13PB7 from UniProtKB/TrEMBL  Length:399

    Alignment length:401
                             1                                                                                                                                                                                                                                                                                                                                                                                                           399 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399 
         Q13PB7_PARXL     - -MKVVSVDTLCCDAGWRNYHFVKLTTDEGIVGWSEFDEGFGSPGVTAVIEQLGKRLVGASVMEHERFFAEAYCLTRPATGGVVSEGIGAIENALLDAKAKTLNVPCYELLGGKLRDRVPVYWSHCPTWRINHPKFFGPPVTDLDGVKRTAEEARERQFRAIKTNIFIHDDGPLHAWRPGFAVPFQPALNVDRKVLRNLRAHLEALRDGAGPDVEILLDLNFNAKPEGYLKILRELADFDLFWVEIDSYSPQGLAYVRNHSPHPISSCETLFGIREFKPFFDANAVDVAIVDTIWNGVWQSMKIAAFADAHDINVAPHNFYGHLCTMINANFAAAVPNLRIMETDIDRLAWEDELFTHAPEYQNGELIIPDRPGWGTDPVEEAILAHPPKVMGGLLQYKRS-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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......hhhhhh.....ee..eee...........hhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sn0 A   0 SLKVVSVDTLCCDAGWRNYHFVKLTTDEGIVGWSEFDEGFGSPGVTAVIEQLGKRLVGASVmEHERFFAEAYCLTRPATGGVVSEGIGAIENALLDAKAKTLNVPCYELLGGKLRDRVPVYWSHCPTWRINHPKFFGPPVTDLDGVKRTAEEARERQFRAIKTNIFIHDDGPLHAWRPGFAVPFQPALNVDRKVLRNLRAHLEALRDGAGPDVEILLDLNFNAKPEGYLKILRELADFDLFWVEIDSYSPQGLAYVRNHSPHPISSCETLFGIREFKPFFDANAVDVAIVDTIWNGVWQSmKIAAFADAHDINVAPHNFYGHLCTmINANFAAAVPNLRImETDIDRLAWEDELFTHAPEYQNGELIIPDRPGWGTDPVEEAILAHPPKVmGGLLQYKRSE 400
                                     9        19        29        39        49        59 |      69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299|      309       319     | 329       339|      349       359       369       379       389|      399 
                                                                                        61-MSE                                                                                                                                                                                                                                        300-MSE                  325-MSE        340-MSE                                           390-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 3SN0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SN0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SN0)

(-) 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ 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
  3sn0
    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: 2oo6 3go2 3sn1 3sn4

(-) Related Entries Specified in the PDB File

2oo6 RELATED ID: NYSGXRC-9228C RELATED DB: TARGETDB
3go2