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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE BOUND TO A NOVEL INHIBITOR
 
Authors :  M. T. Hilgers
Date :  08 Nov 12  (Deposition) - 18 Sep 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthetase, Protein-Inhibitor Complex, Antibacterial, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Teng, M. T. Hilgers, M. L. Cunningham, A. Borchardt, J. B. Locke, S. Abraham, G. Haley, B. P. Kwan, C. Hall, G. W. Hough, K. J. Shaw, J. Finn
Identification Of Bacteria-Selective Threonyl-Trna Synthetase Substrate Inhibitors By Structure-Based Design.
J. Med. Chem. V. 56 1748 2013
PubMed-ID: 23362938  |  Reference-DOI: 10.1021/JM301756M

(-) Compounds

Molecule 1 - THREONINE--TRNA LIGASE
    Chains: A, B
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21-AI
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 242-642
    Gene: THRS, B1719, JW1709
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: THREONYL-TRNA SYNTHETASE, THRRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1X162Ligand/IonN-{[3-(4-AMINO-2-METHYLQUINAZOLIN-7-YL)PHENYL]SULFONYL}-L-THREONINAMIDE
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:334 , HIS A:385 , HIS A:511BINDING SITE FOR RESIDUE ZN A 701
2AC2SOFTWAREMET A:332 , CYS A:334 , ARG A:363 , GLU A:365 , MET A:374 , ARG A:375 , VAL A:376 , PHE A:379 , GLN A:381 , ASP A:383 , HIS A:385 , TYR A:462 , LYS A:465 , GLN A:479 , THR A:482 , GLN A:484 , HIS A:511 , GLY A:516 , SER A:517 , ARG A:520 , ZN A:701 , HOH A:828 , HOH A:871 , HOH A:1032BINDING SITE FOR RESIDUE X16 A 702
3AC3SOFTWARECYS B:334 , HIS B:385 , HIS B:511BINDING SITE FOR RESIDUE ZN B 701
4AC4SOFTWAREMET B:332 , CYS B:334 , ARG B:363 , GLU B:365 , MET B:374 , ARG B:375 , VAL B:376 , PHE B:379 , GLN B:381 , ASP B:383 , HIS B:385 , TYR B:462 , LYS B:465 , GLN B:479 , GLN B:484 , HIS B:511 , SER B:517 , ARG B:520 , ZN B:701 , HOH B:826 , HOH B:931 , HOH B:1042BINDING SITE FOR RESIDUE X16 B 702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:351 -Pro A:352
2Leu B:351 -Pro B:352

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HWP)

(-) 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:409
                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4hwpa1 A:242-532 automated matches                                                                                                                                                                                                                                                                d4hwpa2 A:533-650 automated matches                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeeeeeeee...hhhhh.......eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhh....eee.........eeeeeee.....eeeeeeeeee.hhhhhh...ee.....ee..eeeeeeeeeehhhhhhhhhhhh....hhhhh...eeeee.hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hwp A 242 RDHRKIGKQLDLYHMQEEAPGMVFWHNDGWTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYKDAMFTTSSENREYCIKPMNCPGHVQIFNQGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTEEQIRDEVNGCIRLVYDMYSTFGFEKIVVKLSTRPEKRIGSDEMWDRAEADLAVALEENNIPFEYQLGEGAFYGPKIEFTLYDCLDRAWQCGTVQLDFSLPSRLSASYVGEDNERKVPVMIHRAILGSMERFIGILTEEFAGFFPTWLAPVQVVIMNITDSQSEYVNELTQKLSNAGIRVKADLRNEKIGFKIREHTLRRVPYMLVCGDKEVESGKVAVRTRRGKDLGSMDVNEVIEKLQQEIRSRSLKQLEELEHHHHHH 650
                                   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       521       531       541       551       561       571       581       591       601       611       621       631       641         


Chain B from PDB  Type:PROTEIN  Length:398
                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4hwpb1 B:242-532 automated matches                                                                                                                                                                                                                                                                d4hwpb2 B:533-639 automated matches                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeeeeeeee...hhhhh.......eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhh...eeee.........eeeeeee.....eeeeeeeeee.hhhhhh...ee.....ee..eeeeeeeeeehhhhhhhhhhhhh...hhhhh...eeeee.hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hwp B 242 RDHRKIGKQLDLYHMQEEAPGMVFWHNDGWTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYKDAMFTTSSENREYCIKPMNCPGHVQIFNQGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTEEQIRDEVNGCIRLVYDMYSTFGFEKIVVKLSTRPEKRIGSDEMWDRAEADLAVALEENNIPFEYQLGEGAFYGPKIEFTLYDCLDRAWQCGTVQLDFSLPSRLSASYVGEDNERKVPVMIHRAILGSMERFIGILTEEFAGFFPTWLAPVQVVIMNITDSQSEYVNELTQKLSNAGIRVKADLRNEKIGFKIREHTLRRVPYMLVCGDKEVESGKVAVRTRRGKDLGSMDVNEVIEKLQQEIRSRSLKQ 639
                                   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       521       531       541       551       561       571       581       591       601       611       621       631
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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    Leu A:351 - Pro A:352   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYT_ECOLI | P0A8M3: 1evk 1evl 1fyf 1kog 1qf6 1tje 1tke 1tkg 1tky 4hwo 4hwr 4hws 4p3o 4p3p

(-) Related Entries Specified in the PDB File

4hwo 4hwr 4hws 4hwt