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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-PHENYLUREA (CHEM 1356)
 
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 :  2.55
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
    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
    Organism Taxid5691

 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, 20)

Asymmetric Unit (5, 20)
No.NameCountTypeFull Name
1C131Ligand/Ion1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2CAS4Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL9Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1C13-1Ligand/Ion1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS3Ligand/IonDIMETHYL SULFOXIDE
4GOL3Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
Biological Unit 2 (4, 11)
No.NameCountTypeFull Name
1C131Ligand/Ion1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4GOL6Ligand/IonGLYCEROL
5MET-1Mod. Amino AcidMETHIONINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:583 , ARG A:601BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWAREGLY A:573 , TYR A:574 , ASP A:575 , ALA A:576 , LYS A:720 , HOH A:968BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWARETRP A:345 , GLU A:349 , PRO A:464 , GLY A:465BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWAREPHE A:370 , TYR A:526 , DMS A:806BINDING SITE FOR RESIDUE DMS A 804
05AC5SOFTWAREDMS A:806BINDING SITE FOR RESIDUE DMS A 805
06AC6SOFTWARELEU A:444 , ILE A:525 , DMS A:804 , DMS A:805 , HOH A:939BINDING SITE FOR RESIDUE DMS A 806
07AC7SOFTWAREILE A:248 , TYR A:250 , ASP A:287 , TRP A:474 , TYR A:481 , ILE A:519 , HOH A:1059 , HOH A:1063BINDING SITE FOR RESIDUE MET A 807
08AC8SOFTWAREGLU B:343 , LEU B:482 , ARG B:486 , HOH B:999BINDING SITE FOR RESIDUE GOL B 801
09AC9SOFTWAREARG B:583 , ARG B:601BINDING SITE FOR RESIDUE GOL B 802
10BC1SOFTWAREARG B:408 , VAL B:733 , HOH B:962 , HOH B:1055 , HOH B:1067BINDING SITE FOR RESIDUE GOL B 803
11BC2SOFTWAREGLY B:573 , TYR B:574 , ASP B:575 , ALA B:576 , ARG B:719 , LYS B:720BINDING SITE FOR RESIDUE GOL B 804
12BC3SOFTWARETYR A:305 , HIS B:289 , THR B:333 , LYS B:338 , ASN B:458 , TRP B:459 , ALA B:460BINDING SITE FOR RESIDUE GOL B 805
13BC4SOFTWAREPRO B:464 , GLY B:465BINDING SITE FOR RESIDUE GOL B 806
14BC5SOFTWARETYR B:472 , HOH B:1078BINDING SITE FOR RESIDUE DMS B 807
15BC6SOFTWAREPHE B:319 , GLU B:320 , TYR B:324 , ILE B:326BINDING SITE FOR RESIDUE DMS B 808
16BC7SOFTWAREILE 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 , ALA B:477 , TYR B:481 , ILE B:519 , HIS B:523BINDING SITE FOR RESIDUE C13 B 809

(-) SS Bonds  (0, 0)

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

(-) 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 4MVX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MVX)

(-) 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:531
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               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.hhhh....ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee..ee.........hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvx A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKcFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 768
                                   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       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767 
                                                                                                          318-CAS                                                                                                                                                 470-CAS                                                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:533
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee........eee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee.............hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvx B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKcFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311      |321       331       341       351       361       371       381|      394       404       414       424       434       444       454       464     | 474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764   
                                0|                                                                              318-CAS                                                        381|                                                                                  470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                              385                                                                                                                                                                                                                                                                                                                                                                                              

   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 ; only for superseded entry 3TUN: 2,2)

(no "SCOP Domain" information available for 4MVX, only for superseded entry 3TUN replaced by 4MVX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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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 4mvy 4mw0 4mw1 4mw2 4mw4 4mw5 4mw6 4mw7 4mw9 4mwb 4mwc 4mwd 4mwe 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
4mvy
4mw0
4mw1
4mw2
4mw4
4mw5
4mw6
4mw7
4mw9
4mwb
4mwc
4mwd
4mwe