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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN SERYL-TRNA SYNTHETASE IN COMPLEX WITH SER-SA AT 2.9 ANGSTROM RESOLUTION
 
Authors :  X. Xu, X. -L. Yang
Date :  16 Jun 13  (Deposition) - 02 Oct 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Long Alpha-Helices, Seven-Stranded Anti-Parallel Beta-Sheet, Aminoacylation, Trnaser, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Xu, Y. Shi, X. L. Yang
Crystal Structure Of Human Seryl-Trna Synthetase And Ser-Sa Complex Reveals A Molecular Lever Specific To Higher Eukaryotes.
Structure V. 21 2078 2013
PubMed-ID: 24095058  |  Reference-DOI: 10.1016/J.STR.2013.08.021

(-) Compounds

Molecule 1 - SERINE--TRNA LIGASE, CYTOPLASMIC
    ChainsA
    EC Number6.1.1.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET20B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 2-477
    GeneSARS, SERS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERYL-TRNA SYNTHETASE, SERRS, SERYL-TRNA(SER/SEC) SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
3SSA1Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO42Ligand/IonPHOSPHATE ION
3SSA2Ligand/Ion5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:271 , GLU A:273 , ARG A:302 , GLU A:304 , PHE A:316 , ARG A:317 , VAL A:318 , PHE A:321 , LYS A:323 , GLU A:325 , GLU A:391 , LEU A:392 , VAL A:393 , SER A:394 , ASN A:427 , THR A:429 , ALA A:432 , THR A:434 , ARG A:435 , MG A:504BINDING SITE FOR RESIDUE SSA A 501
2AC2SOFTWAREARG A:310 , PHE A:316 , ARG A:317 , ARG A:390 , GLU A:391BINDING SITE FOR RESIDUE PO4 A 502
3AC3SOFTWARELYS A:376 , ASP A:378 , GLU A:391BINDING SITE FOR RESIDUE MG A 503
4AC4SOFTWAREGLU A:246 , SSA A:501BINDING SITE FOR RESIDUE MG A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L87)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:290 -Pro A:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L87)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L87)

(-) Exons   (0, 0)

(no "Exon" information available for 4L87)

(-) 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    
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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:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhheeeeee.........hhhhhhhhh..eehhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhh...eeee...eeehhhhhhhhhhhhhhhh..eeee...........eeeee...hhhhhhh....eee......eeeeeeeeee..................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeeeeehhhhhhh.eee.............eeeeeeeeehhhhhhhhhhhh....eee...............eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l87 A   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPIE 477
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471      

   Legend:   → Mismatch (orange background)
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  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 4L87)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L87)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L87)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        SYSC_HUMAN | P495913vbb 4rqe 4rqf

(-) Related Entries Specified in the PDB File

3vbb CRYSTAL STRUCTURE OF HUMAN SERYL-TRNA SYNTHETASE