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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN WILD TYPE GLYRS BOUND WITH TRNAGLY
 
Authors :  W. Xie, X. Qin, X. Deng, L. Chen, Y. Liu
Date :  10 Oct 15  (Deposition) - 20 Jul 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.93
Chains :  Asym./Biol. Unit :  A,B,C,E
Keywords :  Aminoacyl-Trna Syntheses, Glycyl-Trna Synthetase, Trna, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qin, X. Deng, L. Chen, W. Xie
Crystal Structure Of The Wild-Type Human Glyrs Bound With Trna(Gly) In A Productive Conformation
J. Mol. Biol. V. 428 3603 2016
PubMed-ID: 27261259  |  Reference-DOI: 10.1016/J.JMB.2016.05.018

(-) Compounds

Molecule 1 - GLYCINE--TRNA LIGASE
    Cell Line: HELA CELLS
    Chains: A, B
    EC Number: 6.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 55-739
    Gene: GARS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DIADENOSINE TETRAPHOSPHATE SYNTHETASE,AP-4-A SYNTHETASE, GLYCYL-TRNA SYNTHETASE,GLYRS
 
Molecule 2 - TRNA(GLY)
    Chains: C, E
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1GAP2Ligand/IonGLYCYL-ADENOSINE-5'-PHOSPHATE
2GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3NI2Ligand/IonNICKEL (II) ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:245 , ARG A:277 , GLU A:279 , ILE A:287 , ARG A:288 , VAL A:289 , PHE A:292 , GLU A:296 , GLU A:403 , ILE A:404 , GLY A:406 , ARG A:410 , GLU A:522 , SER A:524 , GLY A:526 , ARG A:529 , A E:76binding site for residue GAP A 701
2AC2SOFTWARETYR A:94 , LYS A:104 , ASN A:274 , GLU A:291 , THR A:293 , ASP B:125 , CYS B:126 , THR B:127binding site for residue SO4 A 702
3AC3SOFTWAREGLU B:245 , ARG B:277 , GLU B:279 , LEU B:286 , ILE B:287 , ARG B:288 , VAL B:289 , PHE B:292 , GLU B:296 , GLU B:403 , ILE B:404 , GLU B:522 , SER B:524 , GLY B:526 , ARG B:529 , HOH B:802 , A C:76binding site for residue GAP B 701
4AC4SOFTWAREU C:8 , G C:9 , G C:12binding site for residue NI C 101
5AC5SOFTWAREU E:8 , G E:9 , G E:12binding site for residue NI E 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E6M)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:61 -Asp A:62
2Leu A:265 -Pro A:266
3Lys B:150 -Asp B:151
4Leu B:265 -Pro B:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E6M)

(-) Exons   (0, 0)

(no "Exon" information available for 5E6M)

(-) 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:519
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..eee.hhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhhhhhhhh..........eee.......eeee....hhhhhhhhhhhhhhh.....eeeeeeeeee.......hhhhh..eeeeeeeeeeehhhhh...hhhhh...eeeeehhhhhhh....eeeehhhhhhh....hhhhhhhhhhhhhhhhhh..hhh.eeeee.hhhhh..eeeeeeeee..eeeeeeeeee...hhhhhhhhhhh....eeee...........eeee..eeeeeeeehhhhhhhhhhhheee.......eee..........eeeee...hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeee.hhhhhh...eeeeee.....eeeee..hhhhhhhhhhhh..hhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e6m A   7 EEVLAPLRLAVRQQGDLVRKLKEDVDKAVAELKARKRVLEAKELALQPKDDIVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAEKPLKEPKFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFEGQETG 678
                                    16        26   ||   42        52        62        72        82        92       102       112       122       132       142    || 226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376      |389       399       409       419       429      |509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669         
                                                  30|                                                                                                           147|                                                                                                                                                              383|                                              436|                                                                                                                                                                           
                                                   37                                                                                                            222                                                                                                                                                               387                                               507                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eee.hhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhh.hhhhheeee.........hhhhhhhhhh..............eeee...eeee.....eeeee....hhhhhhhhhhhhhhh.....eeeeeeeeee.......hhhhh..eeeeeeeeeeehhhhh...hhhhh...eeeeehhhhhh.....eeeehhhhhh.....hhhhhhhhhhhhhhhhhh..hhh.eeeee.hhhhh...eeeeeeeee..eeeeeeeeeee..hhhhhhhhhhh....eeeeeeeee.......eeeeee..eeeeeeeehhhhhhhhhhhheee.......eee..........eeeee......hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...eeeeehhhhhhh...eeeeee.....eeeee..hhhhhhhhhhh...hhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e6m B  64 IVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMYACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAEKPLKEPKTKRFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFEGQETG 678
                                    73        83        93       103       113       123       133       143       153 ||    203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383|      395       405       415       425       435 ||    512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672      
                                                                                                                     155|                                                                                                                                                                                        383|                                                437|                                                                                                                                                                             
                                                                                                                      196                                                                                                                                                                                         386                                                 505                                                                                                                                                                             


Chain C from PDB  Type:RNA  Length:74
                                                                                                          
                 5e6m C   1 gCGCCGCUGGUGUAGUGGUAUCAUGCAAGAUUCCCAUUCUUGCGACCCGGGUUCGAUUCCCGGGCGGCGCACCA  76
                            |       10     || 21        31        41    ||  52        62        72    
                            1-GTP         16|                          46|                            
                                           18                           48                            


Chain E from PDB  Type:RNA  Length:74
                                                                                                          
                 5e6m E   1 gCGCCGCUGGUGUAGUGGUAUCAUGCAAGAUUCCCAUUCUUGCGACCCGGGUUCGAUUCCCGGGCGGCGCACCA  76
                            |       10     || 21        31        41    ||  52        62        72    
                            1-GTP         16|                          46|                            
                                           18                           48
   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 5E6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E6M)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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        GARS_HUMAN | P41250: 2pme 2pmf 2q5h 2q5i 2zt5 2zt6 2zt7 2zt8 2zxf 4kqe 4kr2 4kr3 4qei

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