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
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  THE 2.9 ANGSTROMS CRYSTAL STRUCTURE OF T. THERMOPHILUS SERYL-TRNA SYNTHETASE COMPLEXED WITH TRNA SER
 
Authors :  S. Biou, V. Cusack, A. Yaremchuk, M. Tukalo
Date :  21 Feb 94  (Deposition) - 30 Apr 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,T
Keywords :  Protein-T-Rna Complex, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Biou, A. Yaremchuk, M. Tukalo, S. Cusack
The 2. 9 A Crystal Structure Of T. Thermophilus Seryl-Trna Synthetase Complexed With Trna(Ser).
Science V. 263 1404 1994
PubMed-ID: 8128220
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNASER
    Chains: T
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
 
Molecule 2 - PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11))
    Chains: A, B
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
15MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
2H2U1Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
3PSU1Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1SER)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SER)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe A:205 -Pro A:206
2Leu A:244 -Pro A:245
3Thr A:384 -Pro A:385
4Phe B:705 -Pro B:706
5Leu B:744 -Pro B:745
6Thr B:884 -Pro B:885

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SER)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SER)

(-) Exons   (0, 0)

(no "Exon" information available for 1SER)

(-) 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:372
 aligned with SYS_THET2 | P34945 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:421
                                    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       410       420 
            SYS_THET2     1 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG 421
               SCOP domains d1sera1 A:1-110 Seryl-tRNA synthetase                                                  (SerRS)                d1sera2 A:111-421 Seryl-tRNA synthetase (SerRS)                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1serA01 A:1-102  [code=1.10.287.40, no                                                  name defined] 1serA02 A:103-420 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhhhh.....hhhhhhhhhh..-------------------------------------------------..hhhhhhhhh...............hhh.eeeeee............hhhhhhhh......hhhh.........hhhhhhhhhhhhhhhhhhhh...eeee...eeehhhhhhh......hhh........eee....hhhhhh.....eee.....eeeeeeeeee..................eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhh.....eeeeeeeee....eeeeeeeeee...........eee.....eeeeeeeeeeeeee.................ee..hhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ser A   1 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQ-------------------------------------------------REKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG 421
                                    10        20        30       | -         -         -         -         -       |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       410       420 
                                                                38                                                88                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:421
 aligned with SYS_THET2 | P34945 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:421
                                    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       410       420 
            SYS_THET2     1 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG 421
               SCOP domains d1serb1 B:501-610 Seryl-tRNA synthetase (SerRS)                                                               d1serb2 B:611-921 Seryl-tRNA synthetase (SerRS)                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1serB01 B:501-602  [code=1.10.287.40, no name defined]                                                1serB02 B:603-920 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                         - CATH domains
           Pfam domains (1) Seryl_tRNA_N-1serB01 B:501-605                                                                           --------------------------------------------------------------tRNA-synt_2b-1serB03 B:668-840                                                                                                                                               --------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Seryl_tRNA_N-1serB02 B:501-605                                                                           --------------------------------------------------------------tRNA-synt_2b-1serB04 B:668-840                                                                                                                                               --------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhh.eeeeee............hhhhhhh.......hhhhh.........hhhhhhhhhhhhhhhhhhh...eeee...eeehhhhhhh......hhh........eee....hhhhhh.....eee.....eeeeeeeeee..................eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhh.....eeeeeeeeehhh.eeeeeeeeee.....hhhh..eee.....eeeeeeeeeeeeee.hhhhhhhhh.......ee..hhh.......ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ser B 501 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG 921
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920 


Chain T from PDB  Type:DNA/RNA  Length:65
                                                                                                 
                 1ser T   4 GAGGUGCCCGAGUGGCuGAAGGGAGGUAGGGGGGCCUCCCUCGCGGGuuCGAAUCCCGCCCUCUC  71
                                    13  ||  ||22   ||   47|||||||47P|      |56        66     
                                       16|  ||    26|   47A||||||47P|     54-5MU             
                                        18  ||     42    47B||||||47Q      55-PSU            
                                          20A-H2U         47C||||||                          
                                           20B             47D|||||                          
                                                            47K||||                          
                                                             47L|||                          
                                                              47M||                          
                                                               47N|                          
                                                                47O
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: tRNA_bind_arm (7)
(-)
Clan: tRNA_synt_II (64)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYS_THET2 | P34945)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0004828    serine-tRNA ligase activity    Catalysis of the reaction: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
biological process
    GO:0016260    selenocysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteine, an essential component of glutathione peroxidase and some other proteins.
    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:0006434    seryl-tRNA aminoacylation    The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    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.

 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
    5MU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    H2U  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PSU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1ser)
 
  Cis Peptide Bonds
    Leu A:244 - Pro A:245   [ RasMol ]  
    Leu B:744 - Pro B:745   [ RasMol ]  
    Phe A:205 - Pro A:206   [ RasMol ]  
    Phe B:705 - Pro B:706   [ RasMol ]  
    Thr A:384 - Pro A:385   [ RasMol ]  
    Thr B:884 - Pro B:885   [ RasMol ]  
 

(-) 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 ](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)
Insightii
  RNA: P atoms (spacefill); protein: ribbon
[ mono GIF format | stereo GIF format ]
  RNA: ribbon; protein: ribbon, secondary structure
[ mono GIF format | stereo GIF format ]
  RNA: spacefill; protein: ribbon, secondary structure
[ mono GIF format | stereo GIF format ]

Midas
  spacefill
[ mono GIF format | stereo GIF format ]
  RNA: ribbon, sticks; protein: ribbon, secondary structure
[ mono GIF format | stereo GIF format ]
Distance Plot
  representative atoms: CA, O3*
[ mono GIF format | mono PDF format ]

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ser
    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
  SYS_THET2 | P34945
    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)
  (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
  SYS_THET2 | P34945
    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
        SYS_THET2 | P34945: 1ses 1set 1sry 3err 5eiu 5f7t 5iea

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SER)