Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 O-PHOSPHOSERYL-TRNA KINASE COMPLEXED WITH SELENOCYSTEINE TRNA AND AMPPNP (CRYSTAL TYPE 1)
 
Authors :  Y. Itoh, S. Chiba, S. Sekine, S. Yokoyama
Date :  18 Jan 10  (Deposition) - 28 Jul 10  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Rna Complex, Trna, Atp-Binding, Kinase, Nucleotide-Binding, Transferase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Chiba, Y. Itoh, S. Sekine, S. Yokoyama
Structural Basis For The Major Role Of O-Phosphoseryl-Trna Kinase In The Uga-Specific Encoding Of Selenocysteine
Mol. Cell V. 39 410 2010
PubMed-ID: 20705242  |  Reference-DOI: 10.1016/J.MOLCEL.2010.07.018

(-) Compounds

Molecule 1 - L-SERYL-TRNA(SEC) KINASE
    ChainsA, B
    EC Number2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCOLD II
    Expression System StrainROSETTA 2(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMJ1538
    Organism CommonMETHANOCOCCUS JANNASCHII
    Organism ScientificMETHANOCALDOCOCCUS JANNASCHII
    Organism Taxid243232
    StrainDSM 2661
    SynonymO-PHOSPHOSERYL-TRNA(SEC) KINASE, PSTK
 
Molecule 2 - SELENOCYSTEINE TRNA
    ChainsC, D
    EngineeredYES
    Organism ScientificMETHANOPYRUS KANDLERI
    Organism Taxid2320
    Other DetailsTRNASEC WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE.
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , VAL A:11 , GLY A:12 , LYS A:13 , SER A:14 , ARG A:116 , HOH A:1001 , HOH A:1002BINDING SITE FOR RESIDUE PO4 A 2001
2AC2SOFTWARELEU B:8 , PRO B:9 , GLY B:10 , GLY B:12 , LYS B:13 , SER B:14 , THR B:15 , ARG B:112 , ARG B:116 , THR B:150 , HOH B:1004 , HOH B:1005 , HOH B:1006 , MG B:2004BINDING SITE FOR RESIDUE ANP B 2002
3AC3SOFTWARESER B:14 , HOH B:1004 , HOH B:1005 , HOH B:1006 , ANP B:2002BINDING SITE FOR RESIDUE MG B 2004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ADB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ADB)

(-) 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:250
 aligned with PSTK_METJA | Q58933 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:250
                              1                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
           PSTK_METJA     - --MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSMRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKFYVLEENKNKNNNISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKMEEVDADRVLKEFKDLLNSY 248
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeee.hhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhh...hhhhhhhhhhhh......hhhhh..eeee.....hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3adb A  -1 HHmLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSmRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKmYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKFYVLEENKNKNNNISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKmEEVDADRVLKEFKDLLNSY 248
                              |      8        18        28        38        48        58        68        78   |    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228|      238       248
                              |                                                                               82-MSE                                       128-MSE                                                                                              229-MSE               
                              1-MSE                                                                                                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with PSTK_METJA | Q58933 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:255
                                   1                                                                                                                                                                                                                                                       
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     
           PSTK_METJA     - -------MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSMRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKFYVLEENKNKNNNISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKMEEVDADRVLKEFKDLLNSY 248
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.....hhhhhhhhhhhhhhhh...eeee.hhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh...hhhhhhhhhhhh......hhhhh..eeee.....hhhhhhhhhhhhhh.....--------...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3adb B -10 mNHHHHHmLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNYYNSmRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKmYEKFDEPGKKYKWDEPFLIIDTTKDIDFNEIAKKLIEKSKEIPKF--------KNNNISDKIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKmEEVDADRVLKEFKDLLNSY 248
                            |||    | 3        13        23        33        43        53        63        73        83        93       103       113       123    |  133       143       153       163       173       183       193       203       213       223     | 233       243     
                          -10-MSE  |                                                                               82-MSE                                       128-MSE                                      173      182                                            229-MSE               
                            -9|    |                                                                                                                                                                                                                                                       
                             -4    |                                                                                                                                                                                                                                                       
                                   1-MSE                                                                                                                                                                                                                                                   

Chain C from PDB  Type:RNA  Length:92
                                                                                                                            
                 3adb C   1 GGCCGCCGCCACCGGGGUGGUCCCCGGGCCGGACUUCAGAUCCGGCGCGCCCCGAGUGGGGCGCGGGGUUCAAUUCCCCGCGGCGGCCGCCA  76
                                 ||  8       |19 |      28        38       47A|||||||47K|||||   55        66 ||     74  
                                5A|         16|  |                         47A||||||47J||||||            64| ||         
                                 5B          18  |                          47B||||||47K|||||             66 ||         
                                               20A                           47C||||||47L||||              67A|         
                                                                              47D||||| 47M|||               67B         
                                                                               47E||||  47N||                           
                                                                                47F|||    48|                           
                                                                                 47G||     50                           
                                                                                  47H|                                  
                                                                                   47I                                  

Chain D from PDB  Type:RNA  Length:92
                                                                                                                            
                 3adb D   1 GGCCGCCGCCACCGGGGUGGUCCCCGGGCCGGACUUCAGAUCCGGCGCGCCCCGAGUGGGGCGCGGGGUUCAAUUCCCCGCGGCGGCCGCCA  76
                                 ||  8       |19 |      28        38       47A|||||||47K|||||   55        66 ||     74  
                                5A|         16|  |                         47A||||||47J||||||            64| ||         
                                 5B          18  |                          47B||||||47K|||||             66 ||         
                                               20A                           47C||||||47L||||              67A|         
                                                                              47D||||| 47M|||               67B         
                                                                               47E||||  47N||                           
                                                                                47F|||    48|                           
                                                                                 47G||     50                           
                                                                                  47H|                                  
                                                                                   47I                                  

   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 3ADB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PSTK_METJA | Q58933)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    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.

 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
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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
(no "Cis Peptide Bonds" information available for 3adb)
 

(-) 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
  3adb
    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
  PSTK_METJA | Q58933
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.-
    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
  PSTK_METJA | Q58933
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PSTK_METJA | Q589333a4l 3a4m 3a4n 3adc 3add 3am1

(-) Related Entries Specified in the PDB File

3adc THE SAME PROTEIN-RNA COMPLEX WITH DIFFERENT CELL PARAMETERS
3add THE SAME PROTEIN-RNA COMPLEX WITH DIFFERENT CELL PARAMETERS