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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR CHEM 1325
 
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 :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,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
    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
    FragmentRESIDUES 235-773
    GeneTB10.70.6470
    MutationYES
    Organism ScientificTRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid999953
    Strain927/4 GUTAT10.1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 25)

Asymmetric Unit (6, 25)
No.NameCountTypeFull Name
10P51Ligand/Ion4-{4-[(1H-BENZIMIDAZOL-2-YLMETHYL)AMINO]-6-(2-CHLORO-4-METHOXYPHENOXY)PYRIMIDIN-2-YL}PIPERAZIN-2-ONE
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL15Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 15)
No.NameCountTypeFull Name
10P5-1Ligand/Ion4-{4-[(1H-BENZIMIDAZOL-2-YLMETHYL)AMINO]-6-(2-CHLORO-4-METHOXYPHENOXY)PYRIMIDIN-2-YL}PIPERAZIN-2-ONE
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL8Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (4, 10)
No.NameCountTypeFull Name
10P51Ligand/Ion4-{4-[(1H-BENZIMIDAZOL-2-YLMETHYL)AMINO]-6-(2-CHLORO-4-METHOXYPHENOXY)PYRIMIDIN-2-YL}PIPERAZIN-2-ONE
2CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS-1Ligand/IonDIMETHYL SULFOXIDE
4GOL7Ligand/IonGLYCEROL
5MET-1Mod. Amino AcidMETHIONINE
6SO41Ligand/IonSULFATE ION
Biological Unit 3 (6, 25)
No.NameCountTypeFull Name
10P51Ligand/Ion4-{4-[(1H-BENZIMIDAZOL-2-YLMETHYL)AMINO]-6-(2-CHLORO-4-METHOXYPHENOXY)PYRIMIDIN-2-YL}PIPERAZIN-2-ONE
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL15Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
6SO41Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:261 , ILE A:265 , HIS A:545 , SER A:585 , GLY A:586 , PHE A:587 , ASP A:660 , ILE A:661 , GLN A:662BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWARETRP A:345 , GLU A:349 , PRO A:464 , GLY A:465BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWAREARG A:271 , PRO A:718 , HOH A:946BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWAREPRO A:429 , GLU A:430 , ASP A:660 , LYS A:663 , GLU B:637 , ASP B:681BINDING SITE FOR RESIDUE GOL A 804
05AC5SOFTWAREARG A:583 , ARG A:601BINDING SITE FOR RESIDUE GOL A 805
06AC6SOFTWAREHIS A:395 , VAL A:396 , HOH A:991BINDING SITE FOR RESIDUE GOL A 806
07AC7SOFTWAREASN A:252 , HIS A:256 , LYS A:292 , SER A:366 , HIS A:395 , ASP A:551BINDING SITE FOR RESIDUE GOL A 807
08AC8SOFTWAREDMS A:809 , DMS A:811BINDING SITE FOR RESIDUE DMS A 808
09AC9SOFTWAREGLU A:392 , LYS A:517 , ASP A:518 , LEU A:520 , LYS A:521 , DMS A:808BINDING SITE FOR RESIDUE DMS A 809
10BC1SOFTWAREPHE A:370 , PRO A:445 , LYS A:521 , TYR A:526 , DMS A:811BINDING SITE FOR RESIDUE DMS A 810
11BC2SOFTWAREALA A:439 , GLY A:443 , LEU A:444 , DMS A:808 , DMS A:810BINDING SITE FOR RESIDUE DMS A 811
12BC3SOFTWARELYS A:316 , GLU A:320BINDING SITE FOR RESIDUE DMS A 812
13BC4SOFTWARESER A:640 , ALA A:674 , ALA A:677 , TYR A:678 , LYS B:663BINDING SITE FOR RESIDUE GOL A 813
14BC5SOFTWAREPRO A:247 , ILE A:248 , TYR A:249 , TYR A:250 , ASP A:287 , TRP A:474 , ALA A:477 , TYR A:481 , LYS A:550 , HOH A:949BINDING SITE FOR RESIDUE MET A 814
15BC6SOFTWAREARG B:271 , ARG B:274 , SER B:714 , PRO B:718BINDING SITE FOR RESIDUE GOL B 901
16BC7SOFTWAREGLU B:343 , LEU B:482 , ARG B:486 , PHE B:502BINDING SITE FOR RESIDUE GOL B 902
17BC8SOFTWARETYR A:655 , LYS A:663 , GLU B:637 , SER B:640 , ALA B:674BINDING SITE FOR RESIDUE GOL B 903
18BC9SOFTWAREARG B:408 , ALA B:411BINDING SITE FOR RESIDUE SO4 B 904
19CC1SOFTWARETYR A:305 , HIS B:289 , LYS B:338 , ASN B:458 , TRP B:459 , ALA B:460 , CAS B:470BINDING SITE FOR RESIDUE GOL B 905
20CC2SOFTWAREILE 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 , ASN B:480 , TYR B:481 , ILE B:519 , PHE B:522 , HIS B:523 , GOL B:909 , HOH B:1015BINDING SITE FOR RESIDUE 0P5 B 906
21CC3SOFTWAREARG B:583 , ARG B:601BINDING SITE FOR RESIDUE GOL B 907
22CC4SOFTWAREVAL B:436 , LEU B:520 , LYS B:521BINDING SITE FOR RESIDUE GOL B 908
23CC5SOFTWARETYR B:250 , GLN B:291 , LYS B:292 , GLU B:368 , LEU B:456 , 0P5 B:906BINDING SITE FOR RESIDUE GOL B 909

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EG6)

(-) 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 4EG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EG6)

(-) Exons   (0, 0)

(no "Exon" information available for 4EG6)

(-) 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 ...eeee...ee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhhh.....eeeee..hhhhhhhhhhhhhhhhh......eeee............hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg6 A 239 EKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTENT 770
                                   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     ||564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764      
                                                                                                                                                                                                                                                                 470-CAS                                                                             554|                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                      561                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:515
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -----d4eg6b1 B:237-606 automated matches                                                                                                                                                                                                                                                                                                                          d4eg6b2 B:607-767 automated matches                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeee......ee......eeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee........eee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...hhhhh..........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg6 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 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       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762     
                                0|                                                                                                                                        376|                                                                     470-CAS                                                                                                                                                                                                                                                                                                     
                               237                                                                                                                                         398                                                                                                                                                                                                                                                                                                                                                                                 

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EG6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EG6)

(-) 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 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
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