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 MOUSE SELENOCYSTEINE SYNTHASE, SODIUM PHOSPHATE SOAK
 
Authors :  O. M. Ganichkin, M. C. Wahl
Date :  12 Nov 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Disorder-Order Transition, Phosphate-Loop, Pyridoxal Phosphate, Selenocysteine Synthase (Secs, Sepsecs), Soluble Liver Antigen/Liver And Pancreas Antigen (Sla/Lp), Protein Biosynthesis, Selenium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. M. Ganichkin, X. M. Xu, B. A. Carlson, H. Mix, D. L. Hatfield, V. N. Gladyshev, M. C. Wahl
Structure And Catalytic Mechanism Of Eukaryotic Selenocysteine Synthase.
J. Biol. Chem. V. 283 5849 2008
PubMed-ID: 18093968  |  Reference-DOI: 10.1074/JBC.M709342200

(-) Compounds

Molecule 1 - O-PHOSPHOSERYL-TRNA(SEC) SELENIUM TRANSFERASE
    ChainsA
    EC Number2.9.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM-13-SECS
    Expression System StrainBL21 ROSETTA2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentELASTASE-RESISTANT FRAGMENT: RESIDUES 19-468
    GeneSEPSECS, D5ERTD135E
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PO48Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:259 , SER A:260 , LYS A:261 , ARG A:341 , HOH A:624BINDING SITE FOR RESIDUE CL A 501
2AC2SOFTWAREARG A:97 , SER A:98 , GLN A:105 , ARG A:313 , HOH A:504 , HOH A:910 , HOH A:970BINDING SITE FOR RESIDUE PO4 A 502
3AC3SOFTWAREARG A:199 , HIS A:368 , HOH A:666 , HOH A:942BINDING SITE FOR RESIDUE PO4 A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:228 -Pro A:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BCB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BCB)

(-) 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:445
 aligned with SPCS_MOUSE | Q6P6M7 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:445
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462     
           SPCS_MOUSE    23 EARRAHEHLIRLLLEQGKCPEDGWDESTLELFLHELAVMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLNVIKLAGVHSVASCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMVTAGFEPVVIENVLEGDELRTDLKAVEAKIQELGPEHILCLHSTTACFAPRVPDRLEELAVICANYDIPHVVNNAYGLQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNEPFIQDISKMYPGRASASPSLDVLITLLSLGCSGYRKLLKERKEMFVYLSTQLKKLAEAHNERLLQTPHNPISLAMTLKTIDGHHDKAVTQLGSMLFTRQVSGARAVPLGNVQTVSGHTFRGFMSHADNYPCAYLNAAAAIGMKMQDVDLFIKRLDKCLNIVRKEQTR 467
               SCOP domains d3bcba_ A: Selenocysteinyl-tRNA synthase (SepSecS)                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..............hhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeeeehhhhhh.....eeeee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.........hhhhhhhhhhhhh.....eee....eeee..eeee............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bcb A  23 EARRAHEHLIRLLLEQGKCPEDGWDESTLELFLHELAVMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLNVIKLAGVHSVASCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMVTAGFEPVVIENVLEGDELRTDLKAVEAKIQELGPEHILCLHSTTACFAPRVPDRLEELAVICANYDIPHVVNNAYGLQSSKCMHLIQQGARVGRIDAFVQSLDkNFMVPVGGAIIAGFNEPFIQDISKMYPGRASASPSLDVLITLLSLGCSGYRKLLKERKEMFVYLSTQLKKLAEAHNERLLQTPHNPISLAMTLKTIDGHHDKAVTQLGSMLFTRQVSGARAVPLGNVQTVSGHTFRGFMSHADNYPCAYLNAAAAIGMKMQDVDLFIKRLDKCLNIVRKEQTR 467
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 |     292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462     
                                                                                                                                                                                                                                                                                               284-LLP                                                                                                                                                                                   

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (SPCS_MOUSE | Q6P6M7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016785    transferase activity, transferring selenium-containing groups    Catalysis of the transfer of a selenium-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0001514    selenocysteine incorporation    The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
    GO:0097056    selenocysteinyl-tRNA(Sec) biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteinyl-tRNA(Sec). This process occurs through the following steps: a unique serine-tRNA with a UGA recognizing anticodon is first aminoacylated with serine; this is then phosphorylated by phosphoseryl-tRNA[Ser]Sec kinase; lastly, selenium is swapped for the phosphate on the serine.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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 ]
    LLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:228 - Pro A:229   [ 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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3bcb
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPCS_MOUSE | Q6P6M7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.9.1.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SPCS_MOUSE | Q6P6M7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPCS_MOUSE | Q6P6M73bc8 3bca

(-) Related Entries Specified in the PDB File

3bc8 CRYSTAL STRUCTURE OF MOUSE SELENOCYSTEINE SYNTHASE
3bca CRYSTAL STRUCTURE OF MOUSE SELENOCYSTEINE SYNTHASE, SODIUM IODIDE SOAK