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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR CHEM 1289
 
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 :  3.15
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, Ligase-Ligase Inhibitor Complex (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  (6, 33)

Asymmetric Unit (6, 33)
No.NameCountTypeFull Name
10OT1Ligand/Ion2-({3-[(3,5-DIBROMO-2-ETHOXYBENZYL)AMINO]PROPYL}AMINO)QUINOLIN-4(1H)-ONE
2CAS4Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS6Ligand/IonDIMETHYL SULFOXIDE
4GOL20Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 19)
No.NameCountTypeFull Name
10OT-1Ligand/Ion2-({3-[(3,5-DIBROMO-2-ETHOXYBENZYL)AMINO]PROPYL}AMINO)QUINOLIN-4(1H)-ONE
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4GOL12Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (5, 14)
No.NameCountTypeFull Name
10OT1Ligand/Ion2-({3-[(3,5-DIBROMO-2-ETHOXYBENZYL)AMINO]PROPYL}AMINO)QUINOLIN-4(1H)-ONE
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4GOL8Ligand/IonGLYCEROL
5MET-1Mod. Amino AcidMETHIONINE
6SO41Ligand/IonSULFATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:345 , GLU A:349 , TYR A:405 , PRO A:464 , GLY A:465 , ASN A:466BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWAREARG A:271 , PRO A:718 , SER A:721 , VAL A:722 , HOH A:928 , HOH A:938BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWAREPRO A:731 , GLU A:732BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWAREARG A:583 , ARG A:601BINDING SITE FOR RESIDUE GOL A 804
05AC5SOFTWAREHIS A:395 , VAL A:396 , HOH A:954BINDING SITE FOR RESIDUE GOL A 805
06AC6SOFTWAREPHE A:741 , HOH A:933 , HOH A:939BINDING SITE FOR RESIDUE GOL A 806
07AC7SOFTWAREPRO A:445 , ASP A:446BINDING SITE FOR RESIDUE GOL A 807
08AC8SOFTWAREGLY A:573 , TYR A:574 , ASP A:575 , HOH A:901BINDING SITE FOR RESIDUE GOL A 808
09AC9SOFTWARESER A:585 , GLY A:586 , PHE A:587 , PRO A:659 , ASP A:660 , ILE A:661 , GLN A:662BINDING SITE FOR RESIDUE GOL A 809
10BC1SOFTWAREASN A:252 , ALA A:253 , HIS A:256 , LYS A:292 , LYS A:550 , ASP A:551 , ARG A:552BINDING SITE FOR RESIDUE GOL A 810
11BC2SOFTWAREHIS A:734 , PRO A:747 , HOH A:917BINDING SITE FOR RESIDUE GOL A 811
12BC3SOFTWAREDMS A:813 , DMS A:815BINDING SITE FOR RESIDUE DMS A 812
13BC4SOFTWAREGLU A:392 , LYS A:517 , ASP A:518 , LEU A:520 , LYS A:521 , DMS A:812BINDING SITE FOR RESIDUE DMS A 813
14BC5SOFTWAREPHE A:370 , LEU A:447 , TYR A:526 , DMS A:815BINDING SITE FOR RESIDUE DMS A 814
15BC6SOFTWARELYS A:521 , DMS A:812 , DMS A:814BINDING SITE FOR RESIDUE DMS A 815
16BC7SOFTWAREPRO A:429 , GLU A:430 , ASP A:660 , LYS A:663 , GLU B:637 , ASP B:681BINDING SITE FOR RESIDUE GOL A 816
17BC8SOFTWAREILE A:248 , TYR A:249 , TYR A:250 , ASP A:287 , TRP A:474 , ALA A:477 , LEU A:478 , HIS A:523 , LYS A:550BINDING SITE FOR RESIDUE MET A 817
18BC9SOFTWAREPHE B:319 , ILE B:326BINDING SITE FOR RESIDUE DMS B 801
19CC1SOFTWAREARG B:271 , ARG B:274 , SER B:714 , LYS B:736BINDING SITE FOR RESIDUE GOL B 802
20CC2SOFTWAREARG B:486BINDING SITE FOR RESIDUE GOL B 803
21CC3SOFTWAREARG B:601BINDING SITE FOR RESIDUE GOL B 804
22CC4SOFTWARELYS B:342 , GLY B:465BINDING SITE FOR RESIDUE GOL B 805
23CC5SOFTWAREHIS B:289 , LYS B:338 , ALA B:460 , HOH B:933BINDING SITE FOR RESIDUE GOL B 806
24CC6SOFTWAREGLY B:573 , TYR B:574 , LYS B:720 , HOH B:916BINDING SITE FOR RESIDUE GOL B 807
25CC7SOFTWAREGLU B:435 , LYS B:521BINDING SITE FOR RESIDUE GOL B 809
26CC8SOFTWARETYR B:472 , 0OT B:812 , HOH B:964BINDING SITE FOR RESIDUE DMS B 810
27CC9SOFTWARETYR B:249 , TYR B:250 , HIS B:259 , 0OT B:812BINDING SITE FOR RESIDUE SO4 B 811
28DC1SOFTWARETYR 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 , DMS B:810 , SO4 B:811BINDING SITE FOR RESIDUE 0OT B 812

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EG4)

(-) 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 4EG4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EG4)

(-) Exons   (0, 0)

(no "Exon" information available for 4EG4)

(-) 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:522
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee.......hhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.hhhh....ee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhh.......eeee..........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eg4 A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKcFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 768
                                   247       257       267       277       287       297       307       317|      327       337       347       357       367       377    || 388       398       408       418       428       438       448       458       468 |     478       488       498       508       518       528       538       548    || 566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766  
                                                                                                          318-CAS                                                         382|                                                                                   470-CAS                                                                            553|                                                                                                                                                                                                              
                                                                                                                                                                           384                                                                                                                                                                       562                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee......eeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee........eee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhhh.....eeeee..hhhhhhhhhhhhhhhhh......eeee...hhhhh........hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg4 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKcFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISLGNVFDPVEKAEEFGYDALKYFLLRESGDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311      |321       331       341       351       361       371    || 402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552  ||   564       574       584 ||    596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766 
                                0|                                                                              318-CAS                                                   376|                                                                     470-CAS                                                                              555|                         586|                                                                                                                                                                                  
                               237                                                                                                                                         398                                                                                                                                                           558                          589
   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 4EG4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EG4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EG4)

(-) Gene Ontology  (10, 10)

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 Related Entries

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

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        Q38C91_TRYB2 | Q38C91: 5tqu
UniProtKB/TrEMBL
        Q38C91_TRYB2 | Q38C91: 4eg1 4eg3 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
4eg3 THE SAME PROTEIN IN COMPLEX WITH PRODUCT METHIONYL-ADENYLATE
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