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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN 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 :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthetase, Protein-Inhibitor Complex, 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, CYTOPLASMIC
    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 321-723
    Gene: TARS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    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
11B22Ligand/IonN-{[3-(2H-INDAZOL-5-YL)PHENYL]SULFONYL}-L-THREONINAMIDE
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:446 , HIS A:497 , HIS A:623 , 1B2 A:802BINDING SITE FOR RESIDUE ZN A 801
2AC2SOFTWAREMET A:444 , CYS A:446 , ARG A:475 , GLN A:493 , ASP A:495 , HIS A:497 , TYR A:573 , ASP A:578 , ILE A:579 , GLN A:590 , CYS A:591 , ALA A:592 , GLN A:595 , HIS A:623 , ZN A:801 , HOH A:918BINDING SITE FOR RESIDUE 1B2 A 802
3AC3SOFTWARECYS B:446 , HIS B:497 , HIS B:623 , 1B2 B:802BINDING SITE FOR RESIDUE ZN B 801
4AC4SOFTWAREMET B:444 , CYS B:446 , ARG B:475 , GLN B:493 , ASP B:495 , HIS B:497 , TYR B:573 , LYS B:576 , ASP B:578 , ILE B:579 , GLN B:590 , CYS B:591 , ALA B:592 , THR B:593 , GLN B:595 , HIS B:623 , ZN B:801BINDING SITE FOR RESIDUE 1B2 B 802

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:689 -B:689

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:463 -Pro A:464
2Ala A:677 -Lys A:678
3Leu B:463 -Pro B:464
4Asp B:612 -Gly B:613

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HWT)

(-) 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:395
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4hwta1 A:354-644 automated matches                                                                                                                                                                                                                                                            d4hwta2 A:645-752 automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhhh...hhhhh.eeeee..eee...hhhhh.......eee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhh...eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...........eeeeee...hhhhhhhhhhhhh....hhhhh...eeeee.hhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hwt A 354 RDHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQA 752
                                   363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603      |617       627       637       647       657       667       677       687       697       707       717       727       737       747     
                                                                                                                                                                                                                                                                                          610|                                                                                                                                         
                                                                                                                                                                                                                                                                                           615                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4hwtb1 B:354-644 automated matches                                                                                                                                                                                                                                                                d4hwtb2 B:645-755 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhh....ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeee..eee...hhhhh.......eee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhh...eeee.........eeeeeee.....eeeeeeeeee.hhhhhh...............eeeeee...hhhhhhhhhhhhhh...hhhhh...eeeee.hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hwt B 354 RDHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEE 755
                                   363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753
   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 4HWT)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:677 - Lys A:678   [ RasMol ]  
    Asp B:612 - Gly B:613   [ RasMol ]  
    Leu A:463 - Pro A:464   [ RasMol ]  
    Leu B:463 - Pro B:464   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYTC_HUMAN | P26639: 1wwt 4p3n 4ttv

(-) Related Entries Specified in the PDB File

4hwo 4hwp 4hwr 4hws