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(-) Description

Title :  CRYSTAL STRUCTURE OF ARGINYL-TRNA SYNTHETASE COMPLEXED WITH L-CANAVANINE
 
Authors :  H. S. Kim, C. H. Jo, S. Y. Cha, A. R. Han, K. Y. Hwang
Date :  10 Apr 14  (Deposition) - 23 Jul 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  High Region, Aminoacyl-Trna Synthetase, Atp Binding, Arginine Binding, Trna Binding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Kim, S. Y. Cha, C. H. Jo, A. R. Han, K. Y. Hwang
The Crystal Structure Of Arginyl-Trna Synthetase From Homo Sapiens
Febs Lett. V. 588 2328 2014
PubMed-ID: 24859084  |  Reference-DOI: 10.1016/J.FEBSLET.2014.05.027

(-) Compounds

Molecule 1 - ARGININE--TRNA LIGASE, CYTOPLASMIC
    Chains: A, B
    EC Number: 6.1.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RARS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARGINYL-TRNA SYNTHETASE, ARGRS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GGB2Ligand/IonL-CANAVANINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GGB1Ligand/IonL-CANAVANINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GGB1Ligand/IonL-CANAVANINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:125 , SER A:128 , ASN A:130 , HIS A:139 , HIS A:165 , TYR A:312 , ASP A:316 , VAL A:336 , GLN A:340 , PHE A:344BINDING SITE FOR RESIDUE GGB A 700
2AC2SOFTWAREASP B:125 , SER B:128 , ASN B:130 , HIS B:139 , HIS B:165 , TYR B:312 , ASP B:316 , TYR B:334 , VAL B:336 , GLN B:340 , PHE B:344BINDING SITE FOR RESIDUE GGB B 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q2X)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:407 -Lys A:408
2Glu B:407 -Lys B:408

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q2X)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q2X)

(-) 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:582
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.........eee........eeeehhhhhhhhh.......hhhhhhhhhhhh......eeeeeee...eeeeeehhhhhhhhhhhhhhh...........eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhh...eeee..eeee........eeee......hhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh........eeeeeee..ee...........hhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhh......ee.hhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q2x A  -1 ASMINIISRLQEVFGHAIKAAYPDLENPPLLVTPSQQAKFGDYQCNSAMGISQMLKTKEQKVNPREIAENITKHLPDNECIEKVEIAGPGFINVHLRKDFVSEQLTSLLVNGVQLPALGENKKVIVDFSSPNIAKEMHVGHLRSTIIGESISRLFEFAGYDVLRLNHVGDWGTQFGMLIAHLQDKFPDYLTVSPPIGDLQVFYKESKKRFDTEEEFKKRAYQCVVLLQGKNPDITKAWKLICDVSRQELNKIYDALDVSLIERGESFYQDRMNDIVKEFEDRGFVQVDDGRKIVFVPGCSIPLTIVKSDGGYTYDTSDLAAIKQRLFEEKADMIIYVVDNGQSVHFQTIFAAAQMIGWYDPKVTRVFHAGFGVVLGEDKKKFKTTVRLMDLLGEGLKRSMDKLKEKERDKVLTAEELNAAQTSVAYGCIKYADLSRNRLNDYIFSFDKMLDDRGNTAAYLLYAFTRIRSIARLANIDEEMLQKAARETKILLDHEKEWKLGRCILRFPEILQKILDDLFLHTLCDYIYELATAFTEFYDSCYCVDRQKILKVNMWRMLLCEAVAAVMAKGFDILGIKPVQRM 588
                                     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       258       268       278       288       298       308       318       328       338       348       358       368       378   ||  392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542   || |556       566       576       586  
                                                                                                                                                                                                                                                                                                                                                                                                                         382|                                                                                                                                                            546| ||                                  
                                                                                                                                                                                                                                                                                                                                                                                                                          387                                                                                                                                                             549 ||                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            551|                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             554                                  


Chain B from PDB  Type:PROTEIN  Length:582
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh........eeee........eeeehhhhhhhhhh.....hhhhhhhhhhhh......eeeeeee...eeeeeehhhhhhhhhhhhhhh.........eeeee..........hhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhh...eeee..eeee........eeee......hhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhh........eeee.....ee.............hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh......ee.hhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q2x B  -1 ASMINIISRLQEVFGHAIKAAYPDLENPPLLVTPSQQAKFGDYQCNSAMGISQMLKKEQKVNPREIAENITKHLPDNECIEKVEIAGPGFINVHLRKDFVSEQLTSLLVNGVQLPALNKKVIVDFSSPNIAKEMHVGHLRSTIIGESISRLFEFAGYDVLRLNHVGDWGTQFGMLIAHLQDKFPDYLTVSPPIGDLQVFYKESKKRFDTEEEFKKRAYQCVVLLQGKNPDITKAWKLICDVSRQELNKIYDALDVSLIERGESFYQDRMNDIVKEFEDRGFVQVDDGRKIVFVPGCSIPLTIVKSDGGYTYDTSDLAAIKQRLFEEKADMIIYVVDNGQSVHFQTIFAAAQMIGWYDPKVTRVFHAGFGVVLGEDKKKFKTRETVRLMDLLGEGLKRSMDKLKEKERDKVLTAEELNAAQTSVAYGCIKYADLSRNRLNDYIFSFDKMLDDRGNTAAYLLYAFTRIRSIARLANIDEEMLQKAARETKILLDHEKEWKLGRCILRFPEILQKILDDLFLHTLCDYIYELATAFTEFYDSCYCVDRQTGKLKVNMWRMLLCEAVAAVMAKGFDILGIKPVQRM 588
                                     8        18        28        38        48     || 59        69        79        89        99       109      |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 ||    393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543  ||   556       566       576       586  
                                                                                  54|                                                         116|                                                                                                                                                                                                                                                                     383|                                                                                                                                                             546|  554|                                
                                                                                   56                                                          119                                                                                                                                                                                                                                                                      386                                                                                                                                                              549   556
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4Q2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q2X)

(-) Gene Ontology  (18, 18)

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 Related Entries

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        SYRC_HUMAN | P54136: 4q2t 4q2y 4r3z 4zaj

(-) Related Entries Specified in the PDB File

4q2t 4q2y