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(-) Description

Title :  STRUCTURE OF METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH 1-(4-{4-[(1H-BENZIMIDAZOL-2-YLMETHYL)AMINO]-6-(4,5-DIMETHOXY-2-METHYLPHENOXY) PYRIMIDIN-2-YL}PIPERAZIN-1-YL)ETHANONE
 
Authors :  M. T. Hilgers
Date :  30 Jun 14  (Deposition) - 29 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Synthesis, Aminoacyl-Trna Synthetase, Aminoacylation, Cytosol, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Li, M. T. Hilgers, M. Stidham, V. Brown-Driver, K. J. Shaw, J. Finn
Discovery And Sar Of A Novel Series Of Pyrimidine Antibacterials Targeting Methionyl-Trna Synthetase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: METG, CH52_03385
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
13BG1Ligand/Ion1-(4-{4-[(1H-BENZIMIDAZOL-2-YLMETHYL)AMINO]-6-(4,5-DIMETHOXY-2-METHYLPHENOXY)PYRIMIDIN-2-YL}PIPERAZIN-1-YL)ETHANONE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:11 , ILE A:12 , TYR A:14 , ASP A:51 , HIS A:53 , GLY A:54 , THR A:133 , TYR A:134 , PHE A:220 , VAL A:234 , TYR A:235 , VAL A:236 , TRP A:237 , ASP A:239 , ASN A:243 , TYR A:244 , ILE A:273 , PHE A:276 , ATP A:602 , HOH A:1216 , HOH A:1222 , HOH A:1223 , HOH A:1279BINDING SITE FOR RESIDUE 3BG A 601
2AC2SOFTWAREPRO A:11 , TYR A:13 , HIS A:20 , GLY A:22 , HIS A:23 , SER A:26 , ALA A:270 , GLU A:272 , ILE A:273 , HIS A:299 , GLY A:300 , TRP A:301 , ILE A:302 , LYS A:308 , MET A:309 , SER A:310 , LYS A:311 , 3BG A:601 , MG A:604 , HOH A:1221 , HOH A:1224 , HOH A:1228 , HOH A:1269 , HOH A:1270 , HOH A:1272 , HOH A:1273 , HOH A:1274 , HOH A:1277 , HOH A:1278BINDING SITE FOR RESIDUE ATP A 602
3AC3SOFTWARETHR A:5 , HOH A:726 , HOH A:852 , HOH A:1211 , HOH A:1212 , HOH A:1213BINDING SITE FOR RESIDUE MG A 603
4AC4SOFTWARESER A:310 , ATP A:602 , HOH A:1269 , HOH A:1270BINDING SITE FOR RESIDUE MG A 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gln A:193 -Pro A:194
2Pro A:208 -Gly A:209
3Trp A:262 -Pro A:263
4Asp A:306 -Gly A:307
5Phe A:519 -Pro A:520

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QRE)

(-) 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 ...eeeeeeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhh.eeeeeeeeeee....eeehhhhheeee.......eee........eeeeeeeeee.hhhhhhhhhhhhhhh...ee.hhhhhhhhhhh.......ee.ee.......ee..eeeeeehhhhhhhhhhhhh.......hhhhhhhh...eeeee..hhhhhhhhhhhhhhhh.......eeee..eee..ee.hhhhh...hhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.ee.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhhh........ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qre A   2 AKETFYITTPIYYPSGNLHIGHAYSTVAGDVIARYKRMQGYDVRYLTGTDEHGQKIQEKAQKAGKTEIEYLDEMIAGIKQLWAKLEISNDDFIRTTEERHKHVVEQVFERLLKQGDIYLGEYEGWYSVPDETYYTESQLVDPQYENGKIIGGKSPDSGHEVELVKEESYFFNISKYTDRLLEFYDQNPDFIQPPSRKNEMINNFIKPGLADLAVSRTSFNWGVHVPSNPKHVVYVWIDALVNYISALGYLSDDESLFNKYWPADIHLMAKEIVRFHSIIWPILLMALDLPLPKKVFAHGWILMKDGKMSKSKGNVVDPNILIDRYGLDATRYYLMRELPFGSDGVFTPEAFVERTNFDLANDLGNLVNRTISMVNKYFDGELPAYQGPLHELDEEMEAMALETVKSYTESMESLQFSVALSTVWKFISRTNKYIDETTPWVLAKDDSQKDMLGNVMAHLVENIRYAAVLLRPFLTHAPKEIFEQLNINNPQFMEFSSLEQYGVLTESIMVTGQPKPIFP 520
                                    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       481       491       501       511
   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 4QRE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4QRE)

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  Cis Peptide Bonds
    Asp A:306 - Gly A:307   [ RasMol ]  
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    Phe A:519 - Pro A:520   [ RasMol ]  
    Pro A:208 - Gly A:209   [ RasMol ]  
    Trp A:262 - Pro A:263   [ RasMol ]  
 

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 Related Entries

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        A0A0B6XLD6_S | A0A0B6XLD6: 4qrd

(-) Related Entries Specified in the PDB File

4qrd