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 AN ENOLASE (MANDELATE RACEMASE SUBGROUP, TARGET EFI-502086) FROM AGROBACTERIUM TUMEFACIENS, WITH A SUCCINIMIDE RESIDUE, NA AND PHOSPHATE
 
Authors :  M. W. Vetting, J. T. Bouvier, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Mo S. R. Wasserman, S. Sojitra, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Initiative (Efi)
Date :  27 Feb 12  (Deposition) - 18 Apr 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Enolase, Mandelate Racemase Subgroup, Enzyme Function Initiative, Efi, Structural Genomics, Alpha-Beta-8-Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, J. T. Bouvier, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of An Enolase (Mandelate Racemase Subgroup, Target Efi-502086) From Agrobacterium Tumefaciens With A Succinimide Residue, Na And Phosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE / MUCONATE LACTONIZING ENZYME FAMILY PROTEIN
    Chains: A
    EC Number: 5.1.2.-
    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: ATU0270
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: C58

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2PO41Ligand/IonPHOSPHATE ION
3SNN1Mod. Amino AcidL-3-AMINOSUCCINIMIDE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2PO48Ligand/IonPHOSPHATE ION
3SNN8Mod. Amino AcidL-3-AMINOSUCCINIMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:120 , LYS A:172 , GLU A:216 , HIS A:218 , GLU A:242 , GLU A:268 , HIS A:318 , GLU A:343 , NA A:502 , HOH A:875 , HOH A:948BINDING SITE FOR RESIDUE PO4 A 501
2AC2SOFTWAREGLU A:216 , GLU A:242 , GLU A:268 , PO4 A:501 , HOH A:775 , HOH A:875BINDING SITE FOR RESIDUE NA A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:266 -Ser A:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DXK)

(-) 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:365
 aligned with Q7D1T6_AGRFC | Q7D1T6 from UniProtKB/TrEMBL  Length:400

    Alignment length:400
                                    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       400
         Q7D1T6_AGRFC     1 MKITKLETVRVAERTNLLWVLVHTDEGITGLGETFFGAETVETYVHEYIAPRVIGRDPLQIDLLAQDLVGYLGFRSSGAEVRGNSAFDIALWDIFGKATNQPIAQLLGGFSRREIRTYNTCAGTEYIKKATGQQTANYGLSGGKDYDDLNGFLHRADELAHSLLEDGITAMKIWPFDAAAEKTRGQYISMPDLKSALEPFEKIRKAVGDKMDIMVEFHSMWQLLPAMQIAKALTPYQTFWHEDPIKMDSLSSLTRYAAVSPAPISASETLGSRWAFRDLLETGAAGVVMLDISWCGGLSEARKIASMAEAWHLPVAPHDCTGPVVLCASTHLSLNAPNALVQESVRAFYKTWYRDLVTALPEVKNGMITVPPGAGLGMELHPDIEKTFTVSRRFSDAASI 400
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....eeeeeeee.....eeeeee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eeee..----------------------------------.hhhhhhhhhhh...eeee..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhheeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh...eee....hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhh.....ee.....-..hhhhhh....eee..eee.............hhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxk A   1 MKITKLETVRVAERTNLLWVLVHTDEGITGLGETFFGAETVETYVHEYIAPRVIGRDPLQIDLLAQDLVGYLGFRSSGAEVRGNSAFDIALWDIFGKATNQPIAQLLGGFSRREIRTYNT----------------------------------RADELAHSLLEDGITAMKIWPFDAAAEKTRGQYISMPDLKSALEPFEKIRKAVGDKMDIMVEFHSMWQLLPAMQIAKALTPYQTFWHEDPIKMDSLSSLTRYAAVSPAPISASETLGSRWAFRDLLETGAAGVVMLDISWCGGLSEARKIASMAEAWHLPVAPHdCTGPVVLCASTHLSLNAPNALVQESVRAF-KTWYRDLVTALPEVKNGMITVPPGAGLGMELHPDIEKTFTVSRRFSDAASI 400
                                    10        20        30        40        50        60        70        80        90       100       110       120         -         -         -    |  160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
                                                                                                                                                 120                                155                                                                                                                                                                 319-SNN                      348 |                                                  
                                                                                                                                                                                                                                                                                                                                                                                       350
   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 4DXK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7D1T6_AGRFC | Q7D1T6)
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
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SNN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:266 - Ser A:267   [ 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
  4dxk
    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
  Q7D1T6_AGRFC | Q7D1T6
    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)
  5.1.2.-
    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
  Q7D1T6_AGRFC | Q7D1T6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7D1T6_AGRFC | Q7D1T6: 4dx3

(-) Related Entries Specified in the PDB File

4dn1
4dx3 RELATED ID: EFI-502086 RELATED DB: TARGETTRACK