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(-) Description

Title :  D-AMINOACYL-TRNA DEACYLASE (DTD) FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH GLYCYL-3'-AMINOADENOSINE AT 2.10 ANGSTROM RESOLUTION
 
Authors :  S. B. Routh, S. Ahmad, R. Sankaranarayanan
Date :  04 Apr 16  (Deposition) - 21 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Dtd, Proofreading, Chiral, Enantioselection, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Routh, K. I. Pawar, S. Ahmad, S. Singh, K. Suma, M. Kumar, S. K. Kuncha, K. Yadav, S. P. Kruparani, R. Sankaranarayanan
Elongation Factor Tu Prevents Misediting Of Gly-Trna(Gly) Caused By The Design Behind The Chiral Proofreading Site Of D-Aminoacyl-Trna Deacylase
Plos Biol. V. 14 02465 2016
PubMed-ID: 27224426  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1002465

(-) Compounds

Molecule 1 - D-TYROSYL-TRNA(TYR) DEACYLASE
    Chains: A, B, C, D, E, F, G, H
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PF11_0095
    Organism Scientific: PLASMODIUM FALCIPARUM (ISOLATE 3D7)
    Organism Taxid: 36329
    Strain: ISOLATE 3D7

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1A3G8Ligand/Ion3'-DEOXY-3'-(GLYCYLAMINO)ADENOSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1A3G2Ligand/Ion3'-DEOXY-3'-(GLYCYLAMINO)ADENOSINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1A3G2Ligand/Ion3'-DEOXY-3'-(GLYCYLAMINO)ADENOSINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1A3G2Ligand/Ion3'-DEOXY-3'-(GLYCYLAMINO)ADENOSINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1A3G2Ligand/Ion3'-DEOXY-3'-(GLYCYLAMINO)ADENOSINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:41 , ILE A:43 , SER A:87 , GLN A:88 , PHE A:89 , LYS A:107 , PHE A:137 , GLY A:138 , PRO B:150binding site for residue A3G A 501
2AC2SOFTWAREGLY A:149 , PRO A:150 , LEU B:41 , ILE B:43 , SER B:87 , GLN B:88 , PHE B:89 , LYS B:107 , PHE B:137 , GLY B:138binding site for residue A3G B 501
3AC3SOFTWARELEU C:41 , ILE C:43 , SER C:87 , GLN C:88 , PHE C:89 , LYS C:107 , PHE C:137 , GLY C:138 , GLY D:149 , PRO D:150binding site for residue A3G C 501
4AC4SOFTWAREPRO C:150 , LEU D:41 , ILE D:43 , SER D:87 , GLN D:88 , PHE D:89 , LYS D:107 , PHE D:137 , GLY D:138binding site for residue A3G D 501
5AC5SOFTWAREGLU C:108 , ASN C:110 , LEU E:41 , ILE E:43 , SER E:87 , GLN E:88 , PHE E:89 , LYS E:107 , PHE E:137 , GLY E:138 , PRO F:150binding site for residue A3G E 501
6AC6SOFTWAREPRO E:150 , LEU F:41 , ILE F:43 , SER F:87 , GLN F:88 , PHE F:89 , LYS F:107 , PRO F:109 , ALA F:112 , PHE F:137 , GLY F:138 , HOH F:604binding site for residue A3G F 501
7AC7SOFTWARELEU G:41 , ILE G:43 , SER G:87 , GLN G:88 , PHE G:89 , LYS G:107 , PHE G:137 , GLY G:138 , HOH G:602 , PRO H:150binding site for residue A3G G 501
8AC8SOFTWAREPRO G:150 , LEU H:41 , ILE H:43 , SER H:87 , GLN H:88 , PHE H:89 , LYS H:107 , PHE H:137 , GLY H:138binding site for residue A3G H 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J61)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:149 -Pro A:150
2Gly B:149 -Pro B:150
3Gly C:149 -Pro C:150
4Gly D:149 -Pro D:150
5Gly E:149 -Pro E:150
6Gly F:149 -Pro F:150
7Gly G:149 -Pro G:150
8Gly H:149 -Pro H:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J61)

(-) Exons   (0, 0)

(no "Exon" information available for 5J61)

(-) 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:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j61 A   1 MRVVIQRVKGAILSVRKLEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10      ||29        39        49        59        69        79        89        99       109       119       129       139       149       159 
                                           17|                                                                                                                                     
                                            27                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j61 B   1 MRVVIQRVKGAILSVRKLEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10      ||29        39        49        59        69        79        89        99       109       119       129       139       149       159  
                                           17|                                                                                                                                      
                                            27                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j61 C   1 MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158   
                                           17|                                                                                                                                       
                                            26                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j61 D   1 MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158  
                                           17|                                                                                                                                      
                                            26                                                                                                                                      


Chain E from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.....eeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j61 E   1 MRVVIQRVKGAILSVRKENEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10        28        38        48        58        68        78        88        98       108       118       128       138       148       158  
                                             19|                                                                                                                                    
                                              28                                                                                                                                    


Chain F from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j61 F   1 MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158  
                                           17|                                                                                                                                      
                                            26                                                                                                                                      


Chain G from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j61 G   1 MRVVIQRVKGAILSVRELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10     || 29        39        49        59        69        79        89        99       109       119       129       139       149       159  
                                          16|                                                                                                                                       
                                           26                                                                                                                                       


Chain H from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j61 H   1 MRVVIQRVKGAILSVRKLEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10      ||29        39        49        59        69        79        89        99       109       119       129       139       149       159
                                           17|                                                                                                                                    
                                            27
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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 5J61)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J61)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J61)

(-) Gene Ontology  (9, 9)

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  5j61
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        Q8IIS0_PLAF7 | Q8IIS0: 3knf 3knp 3ko3 3ko4 3ko5 3ko7 3ko9 3kob 3koc 3kod 3lmt 3lmu 3lmv 4nbi 4nbj

(-) Related Entries Specified in the PDB File

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