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(-) Description

Title :  CRYSTAL STRUCTURE OF T. CRUZI HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH 6-BROMOPYRIDIN-3-AMINE (CHEM 475)
 
Authors :  C. -Y. Koh, W. G. J. Hol
Date :  15 Mar 15  (Deposition) - 12 Aug 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
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. M. J. Verlinde, E. Fan, W. G. J. Hol
A Binding Hotspot In The Trypanosoma Cruzi Histidyl-Trna Synthetase Revealed By Fragment-Based Crystallographic Cocktail Screens
Acta Crystallogr. , Sect. D V. 71 1684 2015
PubMed: search  |  Reference-DOI: 10.1107/S1399004715007683

(-) Compounds

Molecule 1 - HISTIDYL-TRNA SYNTHETASE
    Chains: A, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric Unit (5, 19)
No.NameCountTypeFull Name
14JN2Ligand/Ion6-BROMOPYRIDIN-3-AMINE
2DMS5Ligand/IonDIMETHYL SULFOXIDE
3EDO5Ligand/Ion1,2-ETHANEDIOL
4HIS2Mod. Amino AcidHISTIDINE
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (5, 11)
No.NameCountTypeFull Name
14JN1Ligand/Ion6-BROMOPYRIDIN-3-AMINE
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3EDO4Ligand/Ion1,2-ETHANEDIOL
4HIS1Mod. Amino AcidHISTIDINE
5SO42Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:126 , THR A:128 , GLN A:170 , ASN A:172 , ASP A:174 , LEU A:316 , TYR A:318 , TYR A:319 , TYR A:342 , GLY A:359 , PHE A:360 , GLY A:361 , HOH A:619 , HOH A:648 , HOH A:679 , HOH A:687binding site for residue HIS A 501
02AC2SOFTWAREPRO A:125 , CYS A:154 , TRP A:155 , ARG A:156 , GLU A:167 , HIS A:168 , HOH A:697binding site for residue 4JN A 502
03AC3SOFTWARETRP A:193 , ARG A:196 , SER A:197binding site for residue DMS A 503
04AC4SOFTWAREGLU A:96 , LEU A:97 , ILE A:99 , ARG A:100 , TYR A:349 , HOH A:617 , HOH A:671binding site for residue DMS A 504
05AC5SOFTWARETHR A:115 , GLY A:117 , TYR B:157 , ARG B:166binding site for residue EDO A 505
06AC6SOFTWAREHIS A:168 , GLY A:363 , ASP A:364 , CYS A:365 , VAL A:366binding site for residue SO4 A 506
07AC7SOFTWAREARG A:196 , SER A:201 , SER A:202 , TRP A:305 , HOH A:607binding site for residue SO4 A 507
08AC8SOFTWAREARG A:69 , HIS A:76 , HOH A:606 , HOH A:674 , ARG B:69binding site for residue SO4 A 508
09AC9SOFTWAREGLU B:126 , THR B:128 , GLN B:170 , ASN B:172 , ASP B:174 , LEU B:316 , TYR B:318 , TYR B:319 , TYR B:342 , GLY B:359 , PHE B:360 , GLY B:361 , HOH B:620 , HOH B:660 , HOH B:670 , HOH B:678 , HOH B:688binding site for residue HIS B 501
10AD1SOFTWAREPRO B:125 , CYS B:154 , TRP B:155 , ARG B:156 , GLU B:167 , HIS B:168binding site for residue 4JN B 502
11AD2SOFTWARETRP B:193 , ARG B:196 , SER B:197binding site for residue DMS B 503
12AD3SOFTWARELEU B:97 , ARG B:100 , TYR B:349 , HOH B:609binding site for residue DMS B 504
13AD4SOFTWAREGLN A:250 , VAL A:253 , LEU A:254 , PRO B:473 , ARG B:476binding site for residue DMS B 505
14AD5SOFTWARETYR A:157 , ARG A:166 , THR B:115 , GLY B:117binding site for residue EDO B 506
15AD6SOFTWAREPHE B:426 , ALA B:437 , GLN B:451 , LYS B:453binding site for residue EDO B 507
16AD7SOFTWAREPHE B:229 , ALA B:317 , TYR B:319 , ASN B:344 , HOH B:612binding site for residue EDO B 508
17AD8SOFTWAREVAL A:472 , ARG A:476 , GLN B:250 , VAL B:253 , LEU B:254binding site for residue EDO B 509
18AD9SOFTWAREHIS B:168 , GLY B:363 , ASP B:364 , CYS B:365 , VAL B:366binding site for residue SO4 B 510
19AE1SOFTWAREARG B:196 , SER B:201 , SER B:202 , TRP B:305binding site for residue SO4 B 511

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:144 -Pro A:145
2Leu B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YRN)

(-) 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhh.ee.....eee.hhhh....hhhhhh.eeee.....eeee...hhhhhhhhhhhhhhhh...eeeee..eee.........eeeeeeeeee....hhhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eee.............eeeeeee........eeeee..hhhhhh.......eeeeeee.hhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh.eeeeeeehhhhhhh.eeeeee...eeee.hhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yrn A  48 MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEELYIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAKWYSIPQCWRYEAITRRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSSKDVGIKVNSRKVLQTVVEQAGVTSDKFAPVCVIVDKMEPREEVEAQLAVLGLEPTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIPCAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRLRDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLRGFAVPLDRLVH 501
                                    57        67        77        87        97       107       117       127       137       147       157   ||  169       179       189       199       209       219       229       239||     251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451   ||  473    ||
                                                                                                                                           161|                                                                         240|                                                                                                                                                                                                                 455|       478|
                                                                                                                                            164                                                                          243                                                                                                                                                                                                                  468        501


Chain B from PDB  Type:PROTEIN  Length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhh.ee.....eee.hhhh....hhhhhh.eeee.....eeee...hhhhhhhhhhhhhhhh...eeeee..eee.........eeeeeeeeee....hhhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eee.............eeeeeee........eeeee..hhhhhh.......eeeeeee.hhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh.eeeeeeehhhhhhh.eeeeee...eeee.hhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yrn B  48 MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEELYIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAKWYSIPQCWRYEAITRRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSSKDVGIKVNSRKVLQTVVEQAGVTSDKFAPVCVIVDKMEPREEVEAQLAVLLEPTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIPCAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRLRDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLRGFAVPLDRLVH 501
                                    57        67        77        87        97       107       117       127       137       147       157   ||  169       179       189       199       209       219       229       239||     251  ||   262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452  ||   474   ||
                                                                                                                                           161|                                                                         240|        254|                                                                                                                                                                                                    455|       478|
                                                                                                                                            164                                                                          243         256                                                                                                                                                                                                     468        501
   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 4YRN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  6.1.1.21
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 Related Entries

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

(-) Related Entries Specified in the PDB File

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