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 :  CRYSTAL STRUCTURE OF WILD-TYPE CMOA FROM E.COLI
 
Authors :  J. Kim, R. Toro, J. B. Bonanno, R. Bhosle, P. Sampathkumar, S. C. Almo, Ne Structural Genomics Research Consortium (Nysgrc)
Date :  02 Aug 12  (Deposition) - 10 Oct 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,G
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Rossmann Fold, Synthase, Sam Prephenate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kim, H. Xiao, J. B. Bonanno, C. Kalyanaraman, S. Brown, X. Tang, N. F. Al-Obaidi, Y. Patskovsky, P. C. Babbitt, M. P. Jacobson, Y. -S. Lee, S. C. Almo
Structure-Guided Discovery Of The Metabolite Carboxy-Sam That Modulates Trna Function
Nature V. 498 123 2013
PubMed-ID: 23676670  |  Reference-DOI: 10.1038/NATURE12180

(-) Compounds

Molecule 1 - TRNA (CMO5U34)-METHYLTRANSFERASE
    Chains: A, G
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: LIC PET46A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CMOA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 511145
    Strain: K-12 SUBSTR. MG1655

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GEK2Ligand/Ion(2S)-4-[{[(2S,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL}(CARBOXYLATOMETHYL)SULFONIO]-2-AMMONIOBUTANOATE
2SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:69 , ARG A:76 , HIS A:101 , HOH A:419 , HOH A:446 , HOH A:451 , HOH A:582 , HOH A:588BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREPHE A:20 , PHE A:28 , TYR A:39 , GLY A:64 , SER A:66 , ASP A:89 , ASN A:90 , SER A:91 , MET A:94 , GLY A:116 , ASP A:117 , ILE A:118 , ASN A:132 , PHE A:133 , PHE A:137 , LEU A:138 , ARG A:199 , HOH A:401 , HOH A:403 , HOH A:406 , HOH A:417 , HOH A:444 , HOH A:610BINDING SITE FOR RESIDUE GEK A 302
3AC3SOFTWARELYS A:172 , HIS G:225 , ALA G:243 , GLU G:244 , HOH G:546BINDING SITE FOR RESIDUE SO4 G 301
4AC4SOFTWAREALA G:69 , ARG G:76 , HIS G:101 , HOH G:423 , HOH G:429 , HOH G:525 , HOH G:561BINDING SITE FOR RESIDUE SO4 G 302
5AC5SOFTWAREPHE G:20 , PHE G:28 , TYR G:39 , GLY G:64 , SER G:66 , ASP G:89 , ASN G:90 , SER G:91 , MET G:94 , GLY G:116 , ASP G:117 , ILE G:118 , ASN G:132 , PHE G:133 , PHE G:137 , LEU G:138 , ARG G:199 , HOH G:401 , HOH G:402 , HOH G:405 , HOH G:414 , HOH G:563 , HOH G:585BINDING SITE FOR RESIDUE GEK G 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GEK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GEK)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains d4geka_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh......eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeeeeeee..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gek A  18 WTFDERVAEVFPDMIQRSVPGYSNIISMIGMLAERFVQPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRRHIDAYKAPTPVDVIEGDIRDIAIENASMVVLNFTLQFLEPSERQALLDKIYQGLNPGGALVLSEKFSFEDAKVGELLFNMHHDFKRANGYSELEISQKRSMLENVMLTDSVETHKARLHKAGFEHSELWFQCFNFGSLVALKAEDAA 247
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247


Chain G from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains d4gekg_ G: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh......eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gek G  15 LGDWTFDERVAEVFPDMIQRSVPGYSNIISMIGMLAERFVQPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRRHIDAYKAPTPVDVIEGDIRDIAIENASMVVLNFTLQFLEPSERQALLDKIYQGLNPGGALVLSEKFSFEDAKVGELLFNMHHDFKRANGYSELEISQKRSMLENVMLTDSVETHKARLHKAGFEHSELWFQCFNFGSLVALKAED 245
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 24)

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
    GEK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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
(no "Cis Peptide Bonds" information available for 4gek)
 

(-) 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
  4gek
    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
  C3T5M2_ECOLX | C3T5M2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  CMOA_ECOLI | P76290
    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)
  2.1.1.-
    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
  C3T5M2_ECOLX | C3T5M2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CMOA_ECOLI | P76290
    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
        CMOA_ECOLI | P76290: 4iwn

(-) Related Entries Specified in the PDB File

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