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(-) Description

Title :  CRYSTAL STRUCTURE OF T. CRUZI HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH 5-BROMOPYRIDIN-2(1H)-ONE (CHEM 148)
 
Authors :  C. -Y. Koh, W. G. J. Hol
Date :  15 Mar 15  (Deposition) - 19 Aug 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ligase, Aminoacyl-Trna Synthetase, Aars, Hisrs, Trypanosoma Cruzi, Protein-Inhibitor Complex, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Koh, L. Kallur Siddaramaiah, R. M. Ranade, J. Nguyen, T. Jian, Z. Zhang, J. R. Gillespie, F. S. Buckner, C. L. Verlinde, E. Fan, W. G. Ho
A Binding Hotspot In Trypanosoma Cruzi Histidyl-Trna Synthetase Revealed By Fragment-Based Crystallographic Cocktail Screens.
Acta Crystallogr. , Sect. D V. 71 1684 2015
PubMed-ID: 26249349  |  Reference-DOI: 10.1107/S1399004715007683

(-) Compounds

Molecule 1 - HISTIDYL-TRNA SYNTHETASE, PUTATIVE
    Chains: A
    EC Number: 6.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 45-478
    Gene: TC00.1047053507019.40
    Organism Scientific: TRYPANOSOMA CRUZI (STRAIN CL BRENER)
    Organism Taxid: 353153
    Strain: CL BRENER

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
14HS1Ligand/Ion5-BROMOPYRIDIN-2(1H)-ONE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4HIS1Mod. Amino AcidHISTIDINE
5SO43Ligand/IonSULFATE ION
Biological Unit 1 (5, 16)
No.NameCountTypeFull Name
14HS2Ligand/Ion5-BROMOPYRIDIN-2(1H)-ONE
2DMS4Ligand/IonDIMETHYL SULFOXIDE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4HIS2Mod. Amino AcidHISTIDINE
5SO46Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:126 , THR A:128 , GLN A:170 , ASN A:172 , ASP A:174 , LEU A:316 , TYR A:318 , TYR A:319 , GLY A:338 , TYR A:342 , GLY A:359 , PHE A:360 , GLY A:361 , HOH A:611 , HOH A:632 , HOH A:667 , HOH A:688binding site for residue HIS A 501
2AC2SOFTWAREILE A:106 , PRO A:125 , CYS A:154 , TRP A:155 , ARG A:156 , ARG A:165 , GLU A:167 , HIS A:168binding site for residue 4HS A 502
3AC3SOFTWAREARG A:69 , HIS A:76 , HOH A:601binding site for residue SO4 A 503
4AC4SOFTWAREARG A:165 , HIS A:168 , GLY A:363 , ASP A:364 , CYS A:365 , VAL A:366binding site for residue SO4 A 504
5AC5SOFTWAREARG A:196 , SER A:201 , SER A:202 , TRP A:305 , HOH A:697binding site for residue SO4 A 505
6AC6SOFTWAREGLU A:96 , LEU A:97 , ILE A:99 , ARG A:100 , THR A:348 , TYR A:349 , HOH A:674binding site for residue DMS A 506
7AC7SOFTWARETRP A:193 , ARG A:196 , SER A:197 , TYR A:302 , HOH A:661 , HOH A:686binding site for residue DMS A 507
8AC8SOFTWAREGLN A:55 , THR A:115 , GLY A:117 , HIS A:119 , TYR A:157 , ARG A:166binding site for residue EDO A 508

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:503 -A:503

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:144 -Pro A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YRF)

(-) 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:409
                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhh..ee.....eee.hhhh....hhhhhh..eee.....eeee...hhhhhhhhhhhhhhhh...eeeee..eee......eeeeeeeeee....hhhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eee.............eeeeeee........eeeee..hhhhhh.......eeeeeee.hhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh.eeeeeeehhhhhhh.eeeeee...eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yrf A  48 MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEELYIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAKWYSIPQCWRYERRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSSKDVGIKVNSRKVLQTVVEQAGTSDKFAPVCVIVDKMEREEVEAQLAVLGLTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIPCAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRLRDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLRGFAVPLDRLVH 501
                                    57        67        77        87        97       107       117       127       137       147       157||     172       182       192       202       212       222||     233      |246       256|      268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       470       ||
                                                                                                                                        158|                                                        223|            240|         256|                                                                                                                                                                                                  456|      478|
                                                                                                                                         164                                                         225             244          259                                                                                                                                                                                                   469       501
   Legend:   → Mismatch (orange background)
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  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 4YRF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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    Leu A:144 - Pro A:145   [ RasMol ]  
 
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  6.1.1.21
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 Related Entries

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

UniProtKB/TrEMBL
        Q4DA54_TRYCC | Q4DA54: 3hrk 3lc0 4yp0 4ypf 4yrc 4yre 4yrg 4yri 4yrj 4yrk 4yrl 4yrm 4yrn 4yro 4yrp 4yrq 4yrr 4yrs 4yrt

(-) Related Entries Specified in the PDB File

4yp0 4ypf 4yrc 4yre 4yrg 4yri 4yrj 4yrk 4yrl 4yrm 4yrn 4yro 4yrp 4yrq 4yrr 4yrs 4yrt