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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR N-[(4R)-6,8-DICHLORO-1,2,3,4-TETRAHYDROQUINOLIN-4-YL]-N'-(5-FLUORO-3H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE (CHEM 1717)
 
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 :  2.40
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
    Chains: A, B
    EC Number: 6.1.1.10
    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 237-773
    Gene: TB10.70.6470
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 185431
    Strain: 927/4 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  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
14RC1Ligand/IonN-[(4R)-6,8-DICHLORO-1,2,3,4-TETRAHYDROQUINOLIN-4-YL]-N'-(5-FLUORO-3H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4GOL1Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
14RC-1Ligand/IonN-[(4R)-6,8-DICHLORO-1,2,3,4-TETRAHYDROQUINOLIN-4-YL]-N'-(5-FLUORO-3H-IMIDAZO[4,5-B]PYRIDIN-2-YL)PROPANE-1,3-DIAMINE
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS3Ligand/IonDIMETHYL SULFOXIDE
4GOL-1Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
14RC1Ligand/IonN-[(4R)-6,8-DICHLORO-1,2,3,4-TETRAHYDROQUINOLIN-4-YL]-N'-(5-FLUORO-3H-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

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:248 , TYR A:250 , ASP A:287 , TRP A:474 , ALA A:477 , TYR A:481 , HIS A:523 , THR A:549 , LYS A:550 , HOH A:938binding site for residue MET A 801
2AC2SOFTWAREGLU A:435 , ALA A:439 , LYS A:521 , DMS A:803binding site for residue DMS A 802
3AC3SOFTWAREGLU A:392 , LYS A:517 , ASP A:518 , LEU A:520 , LYS A:521 , DMS A:802binding site for residue DMS A 803
4AC4SOFTWARETRP A:345 , GLU A:349 , TYR A:405 , VAL A:463 , PRO A:464binding site for residue DMS A 804
5AC5SOFTWAREPRO B:247 , ILE B:248 , TYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , LEU B:456 , VAL B:471 , TYR B:472 , VAL B:473 , TRP B:474 , ASP B:476 , TYR B:481 , ILE B:519 , PHE B:522 , HOH B:926 , HOH B:946binding site for residue 4RC B 801
6AC6SOFTWAREARG B:583 , ARG B:601 , HOH B:913binding site for residue GOL B 802
7AC7SOFTWAREGLU B:320 , TYR B:324 , SER B:325 , ILE B:326 , HOH B:1154binding site for residue DMS B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZT7)

(-) 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 4ZT7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZT7)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZT7)

(-) 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:521
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zt7 A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTM 801
                                   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  ||   567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767|
                                                                                                                                                                                                                                                                  470-CAS                                                                         550|                                                                                                                                                                                                           767|
                                                                                                                                                                                                                                                                                                                                                   561                                                                                                                                                                                                            801


Chain B from PDB  Type:PROTEIN  Length:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.ee....ee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee..eee..ee.........hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zt7 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361       371       388       398       408       418       428       438       448       458       468 |     478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758         
                                0|                                                                                                                                           379|                                                                                470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                            387
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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 4ZT7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZT7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZT7)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  4zt7
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  6.1.1.10
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q38C91_TRYB2 | Q38C91: 5tqu
UniProtKB/TrEMBL
        Q38C91_TRYB2 | Q38C91: 4eg1 4eg3 4eg4 4eg5 4eg6 4eg7 4eg8 4ega 4mvw 4mvx 4mvy 4mw0 4mw1 4mw2 4mw4 4mw5 4mw6 4mw7 4mw9 4mwb 4mwc 4mwd 4mwe 4zt2 4zt3 4zt4 4zt5 4zt6 5j58 5j59 5j5a

(-) Related Entries Specified in the PDB File

4zt2 4zt3 4zt4 4zt5 4zt6