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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE GST-LIKE DOMAINS COMPLEX OF EPRS-AIMP2
 
Authors :  H. Y. Cho, B. S. Kang
Date :  27 May 15  (Deposition) - 21 Oct 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  E,F  (1x)
Biol. Unit 3:  G,H  (1x)
Biol. Unit 4:  C,D  (1x)
Keywords :  Ligase, Aimp2, Eprs, Gst-Like Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Y. Cho, S. J. Maeng, H. J. Cho, Y. S. Choi, J. M. Chung, S. Lee, H. K. Kim, J. H. Kim, C. Eom, Y. Kim, M. Guo, H. S. Jung, B. S. Kang, S. Kim
Assembly Of Multi-Trna Synthetase Complex Via Heterotetrameric Glutathione Transferase-Homology Domains.
J. Biol. Chem. V. 290 29313 2015
PubMed-ID: 26472928  |  Reference-DOI: 10.1074/JBC.M115.690867

(-) Compounds

Molecule 1 - BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
    Chains: A, C, E, G
    EC Number: 6.1.1.15, 6.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: GST-LIKE DOMAIN, UNP RESIDUES 1-175
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: M1 TO R175 OF EPRS GST-LIKE DOMAIN
    Synonym: BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE, CELL PROLIFERATION-INDUCING GENE 32 PROTEIN, GLUTAMATYL-PROLYL-TRNA SYNTHETASE, GLUTAMYL-TRNA SYNTHETASE, GLURS, PROLYL-TRNA SYNTHETASE
 
Molecule 2 - AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: GST-LIKE DOMAIN, 90-320
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: T90 TO K320 OF AIMP2 GST-LIKE DOMAIN
    Synonym: MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P38, PROTEIN JTV- 1

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):     EF  
Biological Unit 3 (1x):       GH
Biological Unit 4 (1x):   CD    

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU D:232 , SER D:235 , ILE D:239 , HOH D:2008BINDING SITE FOR RESIDUE GOL D1321
2AC2SOFTWARELEU B:232 , SER B:235 , ILE B:239BINDING SITE FOR RESIDUE GOL B1321

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A34)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A34)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A34)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A34)

(-) Exons   (0, 0)

(no "Exon" information available for 5A34)

(-) 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:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhh....eeee.....eeeee..eee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a34 A   3 TLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLARVATTAGLYGSNLMEHTEIDHWLEFSATKLSSCDSFTSTINELNHCLSLRTYLVGNSLSLADLCVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDVS 170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        


Chain B from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeee.....hhhhhhhhhhhhhhh.eeeeeee.......hhhhhh........eeeeeee......eee........eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a34 B 107 DLNSVLGKDYGALKDIVINANPASPPLSLLVLHRLLCEHFRVLSTVHTHSSVKSVPENLLKCFGRQDYQLGFTLIWKNVPKTQMKFSIQTMCPIEGEGNIARFLFSLFGQKHNAVNATLIDSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPWLAGNELTVADVVLWSVLQQISVTVPANVQRWMRSCENLAPFNTALKLLK 320
                                   116       126       136       146       156       166   ||  183       193       203       213       223       233       243       253       263       273       283    || 296       306       316    
                                                                                         170|                                                                                                           288|                            
                                                                                          178                                                                                                            292                            


Chain C from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......hhhhhhhhhhhh.....eee.....eeeee..eee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a34 C   2 ATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLARVATTAGLYGSNLMEHTEIDHWLEFSATKLSSCDSFTSTINELNHCLSLRTYLVGNSLSLADLCVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDVST 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171


Chain D from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhhhhhh...eeeeeee.......hhhhhh......eeeeeee......eee........eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a34 D 110 SVLGALKDIVINANPASPPLSLLVLHRLLCEHFRVLSTVHTHSSVKSVPENLLKCFQDYQLGFTLIWKNVPKTQMKFSIQTMCPIEGEGNIARFLFSLFGQKHNAVNATLIDSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPWLAGNELTVADVVLWSVLQQICSVTVPANVQRWMRSCENLAPFNTALKLLK 320
                               ||  123       133       143       153       163     ||182       192       202       212       222       232       242       252       262       272       282     ||294       304       314      
                             113|                                                169|                                                                                                          288|                             
                              118                                                 179                                                                                                           291                             


Chain E from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhh....eeee.....eeeee..eee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a34 E   3 TLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLARVATTAGLYGSNLMEHTEIDHWLEFSATKLSSCDSFTSTINELNHCLSLRTYLVGNSLSLADLCVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDV 169
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       


Chain F from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee.....hhhhhhhhhhhh....eeeeeee.......hhhhhh........eeeeeee......eee........eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a34 F 107 DLNSVLGGALKDIVINANPASPPLSLLVLHRLLCEHFRVLSTVHTHSSVKSVPENLLKCFGRQDYQLGFTLIWKNVPKTQMKFSIQTMCPIEGEGNIARFLFSLFGQKHNAVNATLIDSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPWLAGNELTVADVVLWSVLQQISVTVPANVQRWMRSCENLAPFNTALKLLK 320
                                  |119       129       139       149       159       169||     186       196       206       216       226       236       246       256       266       276       286 ||    299       309       319 
                                113|                                                  170|                                                                                                           288|                            
                                 117                                                   178                                                                                                            292                            


Chain G from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh....eeeeee...eeeee..eee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a34 G   2 ATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLARVATTAGLYGSNLMEHTEIDHWLEFSATKLSSCDSFTSTINELNHCLSLRTYLVGNSLSLADLCVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDV 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        


Chain H from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee......hhhhhhhhhhhhhh.eeeeeee.....hhhhhh....eeeeeee......eee........eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a34 H 110 SVLGKDALKDIVINANPASPPLSLLVLHRLLCEHFRVLSTVHTHSSSVPENLLKCFYQLGFTLIWKNVPKTQMKFSIQTMCPIEGEGNIARFLFSLFGQKHNAVNATLIDSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPWLAGNELTVADVVLWSVLQQIGSVTVPANVQRWMRSCENLAPFNTALKLL 319
                                 ||121       131       141       151     ||163     ||184       194       204       214       224       234       244       254       264       274       284    || 296       306       316   
                               115|                                    157|      169|                                                                                                         289|                           
                                118                                     160       181                                                                                                          292
   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 5A34)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A34)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A34)

(-) Gene Ontology  (36, 42)

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  5a34
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  AIMP2_HUMAN | Q13155
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  SYEP_HUMAN | P07814
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  6.1.1.15
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  6.1.1.17
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 Related Entries

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

UniProtKB/Swiss-Prot
        AIMP2_HUMAN | Q13155: 4dpg 4ycu 4ycw 5a1n 5a5h
        SYEP_HUMAN | P07814: 1fyj 4hvc 4k86 4k87 4k88 5a1n 5a5h 5bmu 5vad

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5A34)