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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR 1-(3-{[5-CHLORO-3-(PROP-2-EN-1-YL)-2-(PROP-2-EN-1-YLOXY) BENZYL]AMINO}PROPYL)-3-THIOPHEN-3-YLUREA (CHEM 1475)
 
Authors :  C. Y. Koh, J. E. Kim, A. B. Wetzel, W. J. De Van Der Schueren, S. Shibata Z. Zhang, E. Fan, C. L. M. J. Verlinde, W. G. J. Hol
Date :  24 Sep 13  (Deposition) - 30 Apr 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aminoacyl-Trna Synthetase, Aars, Metrs, Parasite, Protein-Inhibitor Complex, Rossmann Fold, Translation, Nucleotide Binding, Ligase- Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Koh, J. E. Kim, A. B. Wetzel, W. J. De Van Der Schueren, S. Shibata, R. M. Ranade, J. Liu, Z. Zhang, J. R. Gillespie, F. S. Buckner, C. L. Verlinde, E. Fan, W. G. Hol
Structures Of Trypanosoma Brucei Methionyl-Trna Synthetase With Urea-Based Inhibitors Provide Guidance For Drug Design Against Sleeping Sickness.
Plos Negl Trop Dis V. 8 E2775 2014
PubMed-ID: 24743796  |  Reference-DOI: 10.1371/JOURNAL.PNTD.0002775

(-) 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
    Organism Taxid: 5691

 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, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
12EN1Ligand/Ion1-(3-{[5-CHLORO-3-(PROP-2-EN-1-YL)-2-(PROP-2-EN-1-YLOXY)BENZYL]AMINO}PROPYL)-3-THIOPHEN-3-YLUREA
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4GOL8Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 10)
No.NameCountTypeFull Name
12EN-1Ligand/Ion1-(3-{[5-CHLORO-3-(PROP-2-EN-1-YL)-2-(PROP-2-EN-1-YLOXY)BENZYL]AMINO}PROPYL)-3-THIOPHEN-3-YLUREA
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS3Ligand/IonDIMETHYL SULFOXIDE
4GOL4Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO41Ligand/IonSULFATE ION
Biological Unit 2 (5, 8)
No.NameCountTypeFull Name
12EN1Ligand/Ion1-(3-{[5-CHLORO-3-(PROP-2-EN-1-YL)-2-(PROP-2-EN-1-YLOXY)BENZYL]AMINO}PROPYL)-3-THIOPHEN-3-YLUREA
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOL4Ligand/IonGLYCEROL
5MET-1Mod. Amino AcidMETHIONINE
6SO41Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:343 , LEU A:344 , LYS A:347 , LEU A:482 , ARG A:486BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWAREARG A:583 , ARG A:601BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWARETYR A:261 , ILE A:265 , HIS A:545 , PHE A:587 , PRO A:659 , ASP A:660 , ILE A:661 , GLN A:662BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWAREASP A:446BINDING SITE FOR RESIDUE GOL A 804
05AC5SOFTWARELYS A:521BINDING SITE FOR RESIDUE DMS A 805
06AC6SOFTWAREGLU A:392 , LYS A:517 , ASP A:518 , ILE A:519 , LEU A:520 , LYS A:521BINDING SITE FOR RESIDUE DMS A 806
07AC7SOFTWAREPHE A:370 , LYS A:521 , TYR A:526BINDING SITE FOR RESIDUE DMS A 807
08AC8SOFTWAREARG A:271 , VAL A:275 , SER A:714BINDING SITE FOR RESIDUE SO4 A 808
09AC9SOFTWAREILE A:248 , TYR A:249 , 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:952BINDING SITE FOR RESIDUE MET A 809
10BC1SOFTWARELEU B:344 , ARG B:486BINDING SITE FOR RESIDUE GOL B 801
11BC2SOFTWAREARG B:583 , ARG B:601BINDING SITE FOR RESIDUE GOL B 802
12BC3SOFTWARETYR A:305 , HIS B:289 , LYS B:338 , ALA B:460BINDING SITE FOR RESIDUE GOL B 803
13BC4SOFTWAREARG B:408 , GLU B:739 , HOH B:973 , HOH B:1033 , HOH B:1034 , HOH B:1035BINDING SITE FOR RESIDUE GOL B 804
14BC5SOFTWARETYR B:324 , ILE B:326 , HOH B:917BINDING SITE FOR RESIDUE DMS B 805
15BC6SOFTWAREARG B:271 , VAL B:275 , SER B:714 , PRO B:718 , HOH B:901BINDING SITE FOR RESIDUE SO4 B 806
16BC7SOFTWAREILE B:248 , TYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , TYR B:472 , VAL B:473 , TRP B:474 , ASP B:476 , LEU B:478 , TYR B:481 , PHE B:522 , HIS B:523BINDING SITE FOR RESIDUE 2EN B 807

(-) SS Bonds  (0, 0)

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

(-) 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 4MWE)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MWE)

(-) 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:526
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhh.eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.hhhh....ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee............hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mwe A 237 KVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 768
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466   |   476       486       496       506       516       526       536       546    || 562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762      
                                                                                                                                                                                                                                                                   470-CAS                                                                          551|                                                                                                                                                                                                                  
                                                                                                                                                                                                                                                                                                                                                     558                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..................eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee........eee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh.....eeeee...ee.............hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhh.hhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mwe B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 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|                                                                                                                                          378|                                                                                 470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                           386
   Legend:   → Mismatch (orange background)
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  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 4MWE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  Q38C91_TRYB2 | Q38C91
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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 4zt2 4zt3 4zt4 4zt5 4zt6 4zt7 5j58 5j59 5j5a

(-) Related Entries Specified in the PDB File

4eg1 METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH SUBSTRATE METHIONINE
4eg3 METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INTERMEDIATE PRODUCT METHIONYL-ADENYLATE
4eg5 METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR CHEM 1312
4mvw
4mvx
4mvy
4mw0
4mw1
4mw2
4mw4
4mw5
4mw6
4mw7
4mw9
4mwb
4mwc
4mwd