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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR N-(3,5-DICHLOROBENZYL)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE (CHEM 1575)
 
Authors :  C. -Y. Koh, W. G. J. Hol
Date :  14 May 15  (Deposition) - 04 May 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, Aminoacyl-Trna Synthetase, Aars, Metrs, Trypanosoma Brucei, Protein-Inhibitor Complex, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhang, C. Y. Koh, R. M. Ranade, S. Shibata, J. R. Gillespie, M. A. Hulverson, W. Huang, J. Nguyen, N. Pendem, M. H. Gelb, C. L. Verlinde, W. G. Hol, F. S. Buckner, E. Fan
5-Fluoroimidazo[4, 5-B]Pyridine Is A Privileged Fragment Tha Conveys Bioavailability To Potent Trypanosomal Methionyl-Trna Synthetase Inhibitors.
Acs Infect Dis. V. 2 399 2016
PubMed-ID: 27627628  |  Reference-DOI: 10.1021/ACSINFECDIS.6B00036

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE
    ChainsA, B
    EC Number6.1.1.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidAVA0421
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 237-773
    GeneTB10.70.6470
    MutationYES
    Organism ScientificTRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid185431
    Strain927/4 GUTAT10.1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
14RP1Ligand/IonN-(3,5-DICHLOROBENZYL)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL3Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
14RP-1Ligand/IonN-(3,5-DICHLOROBENZYL)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4GOL2Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (5, 6)
No.NameCountTypeFull Name
14RP1Ligand/IonN-(3,5-DICHLOROBENZYL)-N'-(1H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOL1Ligand/IonGLYCEROL
5MET-1Mod. Amino AcidMETHIONINE
6SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:392 , LYS A:517 , ASP A:518 , LEU A:520 , LYS A:521 , DMS A:802binding site for residue DMS A 801
02AC2SOFTWARELYS A:521 , DMS A:801 , HOH A:1039binding site for residue DMS A 802
03AC3SOFTWARETRP A:345 , GLU A:349 , TYR A:405 , PRO A:464binding site for residue DMS A 803
04AC4SOFTWAREARG A:271 , VAL A:275 , SER A:714 , PRO A:718binding site for residue DMS A 804
05AC5SOFTWAREILE A:248 , TYR A:250 , ASP A:287 , TRP A:474 , ALA A:477 , TYR A:481 , HIS A:523 , LYS A:550 , HOH A:918binding site for residue MET A 805
06AC6SOFTWAREARG A:583 , ARG A:601binding site for residue GOL A 806
07AC7SOFTWAREHIS A:457 , ASN A:458binding site for residue GOL A 807
08AC8SOFTWAREILE B:248 , TYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , VAL B:471 , TYR B:472 , VAL B:473 , TRP B:474 , ASP B:476 , TYR B:481 , ILE B:519 , SO4 B:803 , HOH B:905 , HOH B:923binding site for residue 4RP B 801
09AC9SOFTWARETYR B:324 , ILE B:326 , HOH B:1080binding site for residue DMS B 802
10AD1SOFTWARE4RP B:801 , HOH B:955 , HOH B:958 , HOH B:978 , HOH B:997binding site for residue SO4 B 803
11AD2SOFTWAREARG B:271 , VAL B:275 , SER B:714 , PRO B:718 , HOH B:929binding site for residue SO4 B 804
12AD3SOFTWAREARG B:583 , ARG B:601binding site for residue GOL B 805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZT2)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Val A:428 -Pro A:429
2Phe A:508 -Pro A:509
3Ile A:658 -Pro A:659
4Val B:428 -Pro B:429
5Phe B:508 -Pro B:509
6Ile B:658 -Pro B:659

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZT2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZT2)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZT2)

(-) 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:517
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zt2 A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEVLFSKRST 767
                                   247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  |    477       487       497       507       517       527       537       547  ||   568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       760       
                                                                                                                                                                                                                                                                  470-CAS                                                                         550|                                                                                                                                                                                               756|        
                                                                                                                                                                                                                                                                                                                                                   562                                                                                                                                                                                                759        

Chain B from PDB  Type:PROTEIN  Length:532
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeee...eeee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh.....eeeee..eee..ee.........hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zt2 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361       371       381|      395       405       415       425       435       445       455       465    |  475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765  
                                0|                                                                                                                                             381|                                                                                 470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                              386                                                                                                                                                                                                                                                                                                                                                                                             

   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 4ZT2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZT2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZT2)

(-) Gene Ontology  (10, 10)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q38C91_TRYB2 | Q38C915tqu
UniProtKB/TrEMBL
        Q38C91_TRYB2 | Q38C914eg1 4eg3 4eg4 4eg5 4eg6 4eg7 4eg8 4ega 4mvw 4mvx 4mvy 4mw0 4mw1 4mw2 4mw4 4mw5 4mw6 4mw7 4mw9 4mwb 4mwc 4mwd 4mwe 4zt3 4zt4 4zt5 4zt6 4zt7 5j58 5j59 5j5a

(-) Related Entries Specified in the PDB File

4zt3 4zt4 4zt5 4zt6 4zt7