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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH PRODUCT METHIONYL-ADENYLATE
 
Authors :  C. Y. Koh, J. E. Kim, S. Shibata, E. Fan, C. L. M. J. Verlinde, W. G. J. Hol
Date :  30 Mar 12  (Deposition) - 12 Sep 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.94
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aminoacyl-Trna Synthetase, Aars, Metrs, Parasite, Ligase, Protein- Inhibitor Complex, Rossmann-Fold, Translation, Nucleotide Binding, , Rossmann Fold, Trna Binding Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Koh, J. E. Kim, S. Shibata, R. M. Ranade, M. Yu, J. Liu, J. R. Gillespie, F. S. Buckner, C. L. Verlinde, E. Fan, W. G. Hol
Distinct States Of Methionyl-Trna Synthetase Indicate Inhibitor Binding By Conformational Selection.
Structure V. 20 1681 2012
PubMed-ID: 22902861  |  Reference-DOI: 10.1016/J.STR.2012.07.011

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE, PUTATIVE
    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: RESIDUES 235-773
    Gene: TB10.70.6470
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 999953
    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  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2GOL11Ligand/IonGLYCEROL
3ME82Ligand/Ion[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] (2S)-2-AZANYL-4-METHYLSULFANYL-BUTANOATE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2GOL7Ligand/IonGLYCEROL
3ME81Ligand/Ion[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] (2S)-2-AZANYL-4-METHYLSULFANYL-BUTANOATE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2GOL4Ligand/IonGLYCEROL
3ME81Ligand/Ion[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] (2S)-2-AZANYL-4-METHYLSULFANYL-BUTANOATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:583 , ARG A:601BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWAREARG A:271 , VAL A:275 , SER A:714 , PRO A:718 , HOH A:906BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWAREASP A:653 , PHE A:741BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWARETRP A:345 , GLU A:349 , TYR A:405 , VAL A:463 , PRO A:464 , GLY A:465BINDING SITE FOR RESIDUE GOL A 804
05AC5SOFTWAREPHE A:370 , LEU A:371 , THR A:372 , PRO A:445 , LYS A:521 , TYR A:526BINDING SITE FOR RESIDUE GOL A 805
06AC6SOFTWAREPRO A:731 , GLU A:732 , GOL A:807BINDING SITE FOR RESIDUE GOL A 806
07AC7SOFTWARETYR A:355 , ARG A:408 , GOL A:806BINDING SITE FOR RESIDUE GOL A 807
08AC8SOFTWAREILE A:248 , TYR A:249 , TYR A:250 , HIS A:256 , GLY A:258 , HIS A:259 , SER A:262 , ASP A:287 , TRP A:474 , GLY A:516 , ASP A:518 , ILE A:519 , HIS A:523 , HIS A:545 , GLY A:546 , TRP A:547 , TRP A:548 , LYS A:554BINDING SITE FOR RESIDUE ME8 A 808
09AC9SOFTWAREARG B:583 , ARG B:601BINDING SITE FOR RESIDUE GOL B 801
10BC1SOFTWAREGLU B:343 , LYS B:347 , ARG B:486BINDING SITE FOR RESIDUE GOL B 802
11BC2SOFTWAREHIS B:289 , THR B:333 , LYS B:338 , TRP B:459BINDING SITE FOR RESIDUE GOL B 803
12BC3SOFTWAREARG B:719BINDING SITE FOR RESIDUE GOL B 804
13BC4SOFTWAREPRO B:247 , ILE B:248 , TYR B:249 , TYR B:250 , HIS B:256 , GLY B:258 , HIS B:259 , SER B:262 , ASP B:287 , TRP B:474 , ALA B:477 , TYR B:481 , GLY B:516 , ASP B:518 , ILE B:519 , HIS B:545 , GLY B:546 , TRP B:547 , TRP B:548 , HOH B:960BINDING SITE FOR RESIDUE ME8 B 805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EG3)

(-) 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 4EG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EG3)

(-) Exons   (0, 0)

(no "Exon" information available for 4EG3)

(-) 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:527
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhh......eeeee...ee..ee.......hhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhh....hhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg3 A 239 EKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                   248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468 |     478       488       498       508       518       528       538       548       558|      570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       
                                                                                                                                                                                                                                                                 470-CAS                                                                                 558|                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                          561                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains -----d4eg3b1 B:237-606 automated matches                                                                                                                                                                                                                                                                                                                                       d4eg3b2 B:607-768 automated matches                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eee....eee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eeehhhhh....ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhh......eeeee...ee..........hhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhh.hhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg3 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 768
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361       371       381|      396       406       416       426       436       446       456       466   |   476       486       496       506       516       526       536       546       556||     569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759         
                                0|                                                                                                                                             381|                                                                                470-CAS                                                                                557|                                                                                                                                                                                                               
                               237                                                                                                                                              387                                                                                                                                                                        561
   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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EG3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EG3)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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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 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 4zt7 5j58 5j59 5j5a

(-) Related Entries Specified in the PDB File

4eg1 THE SAME PROTEIN IN COMPLEX WITH SUBSTRATE METHIONINE
4eg4 THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1289
4eg5 THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1312
4eg6 THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1325
4eg7 THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1331
4eg8 THE SAME PROTEIN IN COMPLEX WITH LOW MOLECULAR WEIGHT FRAGMENT 89
4ega THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1320