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(-) Description

Title :  CRYSTAL STRUCTURE OF T. CRUZI HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH 1-(4-BROMOPHENYL)METHANAMINE (CHEM 707)
 
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, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
1DMS6Ligand/IonDIMETHYL SULFOXIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3HIS2Mod. Amino AcidHISTIDINE
4PZH2Ligand/Ion1-(4-BROMOPHENYL)METHANAMINE
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (5, 8)
No.NameCountTypeFull Name
1DMS2Ligand/IonDIMETHYL SULFOXIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3HIS1Mod. Amino AcidHISTIDINE
4PZH1Ligand/Ion1-(4-BROMOPHENYL)METHANAMINE
5SO43Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
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 , GLY A:338 , TYR A:342 , GLY A:359 , PHE A:360 , GLY A:361 , HOH A:611 , HOH A:619 , HOH A:655binding site for residue HIS A 501
02AC2SOFTWARECYS A:154 , TRP A:155 , ARG A:156 , ARG A:166 , GLU A:167 , HIS A:168 , SO4 A:506binding site for residue PZH A 502
03AC3SOFTWAREARG A:196 , SER A:197 , TYR A:302binding site for residue DMS A 503
04AC4SOFTWAREGLU A:96 , LEU A:97 , ILE A:99 , ARG A:100 , TYR A:349 , HOH A:627binding site for residue DMS A 504
05AC5SOFTWARETHR A:115 , HIS A:119 , 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:366 , PZH A:502 , HOH A:683binding site for residue SO4 A 506
07AC7SOFTWAREARG A:69 , HIS A:76 , HOH A:601 , ARG B:69binding site for residue SO4 A 507
08AC8SOFTWAREARG A:196 , SER A:201 , SER A:202 , TRP A:305binding 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:614 , HOH B:617 , HOH B:643 , HOH B:655binding site for residue HIS B 501
10AD1SOFTWARECYS B:154 , TRP B:155 , ARG B:156 , ARG B:166 , GLU B:167 , HIS B:168 , SO4 B:509 , HOH B:652binding site for residue PZH B 502
11AD2SOFTWAREARG B:196 , SER B:197binding site for residue DMS B 503
12AD3SOFTWAREVAL A:49 , LEU B:97 , ILE B:99 , ARG B:100 , TYR B:349binding site for residue DMS B 504
13AD4SOFTWAREPRO B:473 , ARG B:476binding site for residue DMS B 505
14AD5SOFTWAREVAL A:472 , PRO A:473 , ARG A:476 , LEU B:254binding site for residue DMS B 506
15AD6SOFTWARETYR A:157 , ARG A:166 , THR B:115 , LYS B:116 , GLY B:117 , HIS B:119binding site for residue EDO B 507
16AD7SOFTWAREARG B:196 , SER B:201 , SER B:202 , TRP B:305binding site for residue SO4 B 508
17AD8SOFTWAREHIS B:168 , GLY B:363 , ASP B:364 , CYS B:365 , VAL B:366 , PZH B:502binding site for residue SO4 B 509

(-) SS Bonds  (0, 0)

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

(-) 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 4YRP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YRP)

(-) 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:408
                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               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..hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eee.............eeeeeee........eeeee..hhhhhh.......eeeeeee.hhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh.eeeeeeehhhhhhh.eeeeee....eeee.hhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yrp A  48 MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEELYIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAKWYSIPQCWRYERRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSSKDVGIKVNSRKVLQTVVEQAGVTSDKFAPVCVIVDKEEVEAQLAVLGPTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIPCAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRLRDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLRRGFAVPLDRLVH 501
                                    57        67        77        87        97       107       117       127       137       147       157||     172       182       192       202       212       222       232     ||248      |260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450     ||471      ||
                                                                                                                                        158|                                                                       238|       255|                                                                                                                                                                                                   456|       478|
                                                                                                                                         164                                                                        245        258                                                                                                                                                                                                    468        501


Chain B from PDB  Type:PROTEIN  Length:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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..hhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eee.............eeeeeee........eeeee..hhhhhh.......eeeeeee.hhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh.eeeeeeehhhhhhh.eeeeee...eeee.hhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yrp B  48 MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEELYIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAKWYSIPQCWRYERRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSSKDVGIKVNSRKVLQTVVEQAGVTSDKFAPVCVIVDKEAQLAVLGLEPTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIPCAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRLRDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLRGFAVPLDRLVH 501
                                    57        67        77        87        97       107       117       127       137       147       157||     172       182       192       202       212       222       232     ||251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451    || 473    ||
                                                                                                                                        158|                                                                       238|                                                                                                                                                                                                             456|      478|
                                                                                                                                         164                                                                        248                                                                                                                                                                                                              469       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 4YRP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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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 4yrn 4yro 4yrq 4yrr 4yrs 4yrt

(-) Related Entries Specified in the PDB File

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