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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR 1-(3-{[5-CHLORO-2-HYDROXY-3-(PROP-2-EN-1-YL)BENZYL]AMINO}PROPYL)-3-THIOPHEN-3-YLUREA (CHEM 1472)
 
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 :  2.30
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, 25)

Asymmetric Unit (6, 25)
No.NameCountTypeFull Name
12E91Ligand/Ion1-(3-{[5-CHLORO-2-HYDROXY-3-(PROP-2-EN-1-YL)BENZYL]AMINO}PROPYL)-3-THIOPHEN-3-YLUREA
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL12Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO44Ligand/IonSULFATE ION
Biological Unit 1 (5, 16)
No.NameCountTypeFull Name
12E9-1Ligand/Ion1-(3-{[5-CHLORO-2-HYDROXY-3-(PROP-2-EN-1-YL)BENZYL]AMINO}PROPYL)-3-THIOPHEN-3-YLUREA
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4GOL9Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO41Ligand/IonSULFATE ION
Biological Unit 2 (5, 9)
No.NameCountTypeFull Name
12E91Ligand/Ion1-(3-{[5-CHLORO-2-HYDROXY-3-(PROP-2-EN-1-YL)BENZYL]AMINO}PROPYL)-3-THIOPHEN-3-YLUREA
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOL3Ligand/IonGLYCEROL
5MET-1Mod. Amino AcidMETHIONINE
6SO43Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:587 , PRO A:659 , ASP A:660 , ILE A:661 , GLN A:662BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWAREARG A:583BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWARESER A:366 , LYS A:382 , HIS A:395 , VAL A:396BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWAREPRO A:731 , GLU A:732 , VAL A:733BINDING SITE FOR RESIDUE GOL A 804
05AC5SOFTWARETRP A:345 , TYR A:405 , PRO A:464 , HOH A:927BINDING SITE FOR RESIDUE GOL A 805
06AC6SOFTWAREVAL A:340 , GLU A:343 , LEU A:344 , LYS A:347 , LEU A:482 , ARG A:486BINDING SITE FOR RESIDUE GOL A 806
07AC7SOFTWAREARG A:719BINDING SITE FOR RESIDUE GOL A 807
08AC8SOFTWAREHIS A:289 , THR A:333 , LYS A:338 , ASN A:458 , TRP A:459 , ALA A:460 , CAS A:470BINDING SITE FOR RESIDUE GOL A 808
09AC9SOFTWAREPRO A:445 , ASP A:446BINDING SITE FOR RESIDUE GOL A 809
10BC1SOFTWAREDMS A:812BINDING SITE FOR RESIDUE DMS A 810
11BC2SOFTWAREPHE A:370 , LYS A:521 , TYR A:526BINDING SITE FOR RESIDUE DMS A 811
12BC3SOFTWAREGLU A:435 , LYS A:521 , ILE A:525 , DMS A:810BINDING SITE FOR RESIDUE DMS A 812
13BC4SOFTWAREGLU A:392 , LYS A:517 , ASP A:518 , ILE A:519 , LEU A:520 , LYS A:521BINDING SITE FOR RESIDUE DMS A 813
14BC5SOFTWAREARG A:271 , VAL A:275 , SER A:714 , PRO A:718 , HOH A:969BINDING SITE FOR RESIDUE SO4 A 814
15BC6SOFTWAREILE A:248 , TYR A:250 , ASP A:287 , TRP A:474 , ALA A:477 , ILE A:519 , THR A:549BINDING SITE FOR RESIDUE MET A 815
16BC7SOFTWARETYR A:305 , HIS B:289 , THR B:333 , LYS B:338 , TRP B:459 , ALA B:460BINDING SITE FOR RESIDUE GOL B 801
17BC8SOFTWAREGLU B:343 , LEU B:344 , LEU B:482 , ARG B:486 , LEU B:536 , HOH B:977BINDING SITE FOR RESIDUE GOL B 802
18BC9SOFTWAREARG B:583 , ARG B:601BINDING SITE FOR RESIDUE GOL B 803
19CC1SOFTWAREARG B:271 , VAL B:275 , SER B:714 , PRO B:718 , HOH B:1023BINDING SITE FOR RESIDUE SO4 B 804
20CC2SOFTWARETYR B:249 , TYR B:250 , HIS B:259 , 2E9 B:808BINDING SITE FOR RESIDUE SO4 B 805
21CC3SOFTWAREARG B:408 , VAL B:733BINDING SITE FOR RESIDUE SO4 B 806
22CC4SOFTWAREPHE B:319 , TYR B:324 , ILE B:326 , HOH B:1012BINDING SITE FOR RESIDUE DMS B 807
23CC5SOFTWAREILE B:248 , TYR B:250 , ASP B:287 , HIS B:289 , VAL B:473 , TRP B:474 , ASP B:476 , LEU B:478 , TYR B:481 , ILE B:519 , PHE B:522 , HIS B:523 , SO4 B:805BINDING SITE FOR RESIDUE 2E9 B 808

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MW2)

(-) 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 4MW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MW2)

(-) Exons   (0, 0)

(no "Exon" information available for 4MW2)

(-) 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..hhhhhhhhhhhhhhhhhhh.eeeeeeeeeee....eeehhh.eeeee.....eeeee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mw2 A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 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 ||    567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767 
                                                                                                                                                                                                                                                                  470-CAS                                                                        549|                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                                                                                  560                                                                                                                                                                                                                


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..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee....eeee....eeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee........eee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee.............hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mw2 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|                                                                                                                                             381|                                                                                  470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                              385
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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 4MW2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MW2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MW2)

(-) Gene Ontology  (10, 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 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
4mvx
4mvy
4mw0
4mw1
4mw4
4mw5
4mw6
4mw7
4mw9
4mwb
4mwc
4mwd
4mwe