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(-) Description

Title :  TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR CHEM 1331
 
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 :  2.75
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, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
10P41Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-N'-(3,5-DICHLOROBENZYL)PROPANE-1,3-DIAMINE
2CAS4Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS7Ligand/IonDIMETHYL SULFOXIDE
4GOL17Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
10P4-1Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-N'-(3,5-DICHLOROBENZYL)PROPANE-1,3-DIAMINE
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL6Ligand/IonGLYCEROL
5MET1Mod. Amino AcidMETHIONINE
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
10P41Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-N'-(3,5-DICHLOROBENZYL)PROPANE-1,3-DIAMINE
2CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4GOL11Ligand/IonGLYCEROL
5MET-1Mod. Amino AcidMETHIONINE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:345 , GLU A:349 , TYR A:405 , PRO A:464 , GLY A:465BINDING SITE FOR RESIDUE GOL A 801
02AC2SOFTWAREASP A:726 , GLY A:729 , VAL A:730 , ARG A:735 , HOH A:913BINDING SITE FOR RESIDUE GOL A 802
03AC3SOFTWAREARG A:583 , ARG A:601BINDING SITE FOR RESIDUE GOL A 803
04AC4SOFTWAREPHE A:741BINDING SITE FOR RESIDUE GOL A 804
05AC5SOFTWAREHIS A:289 , LYS A:338 , ASN A:458 , ALA A:460 , TYR B:305BINDING 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:435 , ALA A:439 , DMS A:808 , DMS A:809BINDING SITE FOR RESIDUE DMS A 807
08AC8SOFTWAREGLU A:392 , LYS A:517 , ASP A:518 , LEU A:520 , LYS A:521 , DMS A:807BINDING SITE FOR RESIDUE DMS A 808
09AC9SOFTWARELYS A:521 , ILE A:525 , DMS A:807BINDING SITE FOR RESIDUE DMS A 809
10BC1SOFTWAREPHE A:319 , GLU A:320 , TYR A:324 , ILE A:326BINDING SITE FOR RESIDUE DMS A 810
11BC2SOFTWAREARG A:271 , VAL A:275 , SER A:714 , PRO A:718BINDING SITE FOR RESIDUE DMS A 811
12BC3SOFTWAREILE A:248 , TYR A:250 , ASP A:287 , TRP A:474 , ALA A:477 , ILE A:519 , HIS A:523 , HOH A:1023BINDING SITE FOR RESIDUE MET A 812
13BC4SOFTWAREARG B:271 , SER B:714 , HOH B:1017BINDING SITE FOR RESIDUE GOL B 801
14BC5SOFTWAREGLU B:343 , LEU B:344 , ARG B:486 , HOH B:1046BINDING SITE FOR RESIDUE GOL B 802
15BC6SOFTWAREARG B:408 , ALA B:411 , HOH B:955 , HOH B:956BINDING SITE FOR RESIDUE GOL B 803
16BC7SOFTWAREHIS B:289 , THR B:333 , LYS B:338 , ASN B:458 , TRP B:459 , ALA B:460BINDING SITE FOR RESIDUE GOL B 804
17BC8SOFTWAREARG B:583 , ARG B:601BINDING SITE FOR RESIDUE GOL B 805
18BC9SOFTWAREARG B:719BINDING SITE FOR RESIDUE GOL B 806
19CC1SOFTWAREGLU B:239 , TYR B:359 , PHE B:370 , MET B:406 , ASP B:446BINDING SITE FOR RESIDUE GOL B 807
20CC2SOFTWARELYS B:342 , GLY B:465 , HOH B:1057BINDING SITE FOR RESIDUE GOL B 808
21CC3SOFTWARESER B:556 , LYS B:557 , SER B:558BINDING SITE FOR RESIDUE GOL B 809
22CC4SOFTWAREARG B:358 , SER B:401 , GLU B:403BINDING SITE FOR RESIDUE GOL B 810
23CC5SOFTWARELYS B:720 , PHE B:762 , SER B:763 , ARG B:765 , HOH B:971BINDING SITE FOR RESIDUE GOL B 811
24CC6SOFTWAREGLU B:320 , TYR B:324 , ILE B:326 , HOH B:1010BINDING SITE FOR RESIDUE DMS B 812
25CC7SOFTWARETYR B:472BINDING SITE FOR RESIDUE DMS B 813
26CC8SOFTWAREILE 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 , LEU B:478 , TYR B:481 , ILE B:519 , HOH B:1001 , HOH B:1015BINDING SITE FOR RESIDUE 0P4 B 814

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EG7)

(-) 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 4EG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EG7)

(-) Exons   (0, 0)

(no "Exon" information available for 4EG7)

(-) 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:531
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee......eeeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee.........ee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee.............hhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg7 A 238 VEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKcFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRSTE 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       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767 
                                                                                                          318-CAS                                                                                                                                                 470-CAS                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:536
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.eeeee.....eeeee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh...ee.eee........eee..eeeeeehhhhhhhhhhhhhhheee.....eeee..hhhhh......eeeee..hhhhhhhhhhhhhhhhh......eeee...ee.............hhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhh...hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhh.hhhhhh......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg7 B  -4 GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKcFEQMDYSIDYFIRTTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVDKDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHcVYVWLDALTNYLTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST 767
                                || 241       251       261       271       281       291       301       311      |321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761      
                                0|                                                                              318-CAS                                                                                                                                                 470-CAS                                                                                                                                                                                                                                                                                                     
                               237
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  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 4EG7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EG7)

(-) Gene Ontology  (10, 10)

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  Q38C91_TRYB2 | Q38C91
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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 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
4eg8 THE SAME PROTEIN IN COMPLEX WITH LOW MOLECULAR WEIGHT FRAGMENT 89
4ega THE SAME PROTEIN IN COMPLEX WITH INHIBITOR CHEM 1320