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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR CHEM 1312
 
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 :  3.10
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  (5, 27)

Asymmetric Unit (5, 27)
No.NameCountTypeFull Name
10OU1Ligand/Ion2-({3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}AMINO)QUINOLIN-4(1H)-ONE
2DMS6Ligand/IonDIMETHYL SULFOXIDE
3GOL18Ligand/IonGLYCEROL
4MET1Mod. Amino AcidMETHIONINE
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 17)
No.NameCountTypeFull Name
10OU-1Ligand/Ion2-({3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}AMINO)QUINOLIN-4(1H)-ONE
2DMS5Ligand/IonDIMETHYL SULFOXIDE
3GOL11Ligand/IonGLYCEROL
4MET1Mod. Amino AcidMETHIONINE
5SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (4, 10)
No.NameCountTypeFull Name
10OU1Ligand/Ion2-({3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}AMINO)QUINOLIN-4(1H)-ONE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3GOL7Ligand/IonGLYCEROL
4MET-1Mod. Amino AcidMETHIONINE
5SO41Ligand/IonSULFATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:261 , LEU A:582 , SER A:585 , PHE A:587 , PRO A:659 , ASP A:660 , ILE A:661 , GLN A:662BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWAREARG A:271 , ARG A:274 , VAL A:275BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWAREARG A:583 , ARG A:601BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWAREASP A:381 , HIS A:395 , VAL A:396BINDING SITE FOR RESIDUE GOL A 804
05AC5SOFTWAREPRO A:731 , GLU A:732BINDING SITE FOR RESIDUE GOL A 805
06AC6SOFTWAREGLY A:573 , TYR A:574 , ASP A:575 , ALA A:576 , LYS A:720BINDING SITE FOR RESIDUE GOL A 806
07AC7SOFTWAREGLU A:349 , PRO A:464 , GLY A:465BINDING SITE FOR RESIDUE GOL A 807
08AC8SOFTWARELEU A:344 , LYS A:347 , LEU A:482 , ARG A:486BINDING SITE FOR RESIDUE GOL A 808
09AC9SOFTWAREASN A:252 , HIS A:256 , LYS A:292 , ASP A:551BINDING SITE FOR RESIDUE GOL A 809
10BC1SOFTWAREARG A:719BINDING SITE FOR RESIDUE GOL A 810
11BC2SOFTWAREHIS A:289 , LYS A:338 , ASN A:458 , TRP A:459 , ALA A:460BINDING SITE FOR RESIDUE GOL A 811
12BC3SOFTWAREPHE A:370 , PRO A:445 , LYS A:521 , TYR A:526 , DMS A:813 , HOH A:945BINDING SITE FOR RESIDUE DMS A 812
13BC4SOFTWAREDMS A:812 , DMS A:814BINDING SITE FOR RESIDUE DMS A 813
14BC5SOFTWAREALA A:439 , DMS A:813 , DMS A:815BINDING SITE FOR RESIDUE DMS A 814
15BC6SOFTWAREGLU A:392 , LYS A:517 , LEU A:520 , LYS A:521 , DMS A:814BINDING SITE FOR RESIDUE DMS A 815
16BC7SOFTWARETHR A:284 , PHE A:319 , ILE A:326 , PHE A:329BINDING SITE FOR RESIDUE DMS A 816
17BC8SOFTWAREILE A:248 , TYR A:250 , ASP A:287 , TRP A:474 , ASN A:480 , TYR A:481 , ILE A:519 , HIS A:523 , THR A:549 , LYS A:550BINDING SITE FOR RESIDUE MET A 817
18BC9SOFTWAREGLU B:343 , LEU B:344 , LYS B:347 , LEU B:482 , ARG B:486 , ASP B:500 , HOH B:907BINDING SITE FOR RESIDUE GOL B 801
19CC1SOFTWAREARG B:583 , ARG B:601 , HOH B:972BINDING SITE FOR RESIDUE GOL B 802
20CC2SOFTWAREARG B:408BINDING SITE FOR RESIDUE GOL B 803
21CC3SOFTWAREARG B:271 , ARG B:274 , SER B:714BINDING SITE FOR RESIDUE GOL B 804
22CC4SOFTWAREGLY B:573 , TYR B:574 , ASP B:575 , LYS B:720BINDING SITE FOR RESIDUE GOL B 805
23CC5SOFTWAREGLU A:430 , ASP A:660 , LYS A:663 , GLU B:637 , ASP B:681BINDING SITE FOR RESIDUE GOL B 806
24CC6SOFTWAREARG B:271 , ASP B:323 , ARG B:719BINDING SITE FOR RESIDUE GOL B 807
25CC7SOFTWARETYR B:249 , TYR B:250 , HIS B:259 , 0OU B:810 , HOH B:985BINDING SITE FOR RESIDUE SO4 B 809
26CC8SOFTWARETYR B:250 , ASP B:287 , HIS B:289 , GLY B:290 , LEU B:456 , TYR B:472 , VAL B:473 , TRP B:474 , ASP B:476 , TYR B:481 , ILE B:519 , SO4 B:809 , HOH B:982BINDING SITE FOR RESIDUE 0OU B 810

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EG5)

(-) 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 4EG5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EG5)

(-) Exons   (0, 0)

(no "Exon" information available for 4EG5)

(-) 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 ...eeee...ee.......hhhhhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeee.......eeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee.............eeeee..hhhhhhhhhhhhhhhh.......eeee..........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhh.hhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg5 A 239 EKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 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    || 566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766 
                                                                                                                                                                                                                                                                                                                                                    553|                                                                                                                                                                                                             
                                                                                                                                                                                                                                                                                                                                                     562                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.eee.hhhh....ee..eeeeeehhhhhhhhhhhhhh.eee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhh.......eeee...hhhhh......hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhh.hhhhhh........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg5 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDEWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKIGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRS 766
                                || 241       251       261       271       281       291       301       311       321       331       341       351       361      |401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551   ||  565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765 
                                0|                                                                                                                                368|                                                                                                                                                         555|                                                                                                                                                                                                              
                               237                                                                                                                                 399                                                                                                                                                          560
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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 4EG5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EG5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EG5)

(-) 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 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