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(-) Description

Title :  CRYSTAL STRUCTURE OF METHIONYL-TRNA SYNTHETASE METRS FROM BRUCELLA MELITENSIS IN COMPLEX WITH INHIBITOR 1-{3-[(3,5-DICHLOROBENZYL) AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
 
Authors :  Seattle Structural Genomics Center For Infectious Disease, Se Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  25 Mar 14  (Deposition) - 15 Apr 15  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Ligase, Methionyl-Trna Synthetase, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. K. Ojo, R. M. Ranade, Z. Zhang, D. M. Dranow, J. B. Myers, R. Choi, S. Nakazawa Hewitt, T. E. Edwards, D. R. Davies, D. Lorimer, S. M. Boyle, L. K. Barrett, F. S. Buckner, E. Fan, W. C. Van Voorhis
Brucella Melitensis Methionyl-Trna-Synthetase (Metrs), A Potential Drug Target For Brucellosis.
Plos One V. 11 60350 2016
PubMed-ID: 27500735  |  Reference-DOI: 10.1371/JOURNAL.PONE.0160350

(-) Compounds

Molecule 1 - METHIONINE--TRNA LIGASE
    Chains: A, B, C
    EC Number: 6.1.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: METG, BAB1_1014
    Organism Scientific: BRUCELLA MELITENSIS
    Organism Taxid: 359391
    Strain: 2308
    Synonym: METHIONYL-TRNA SYNTHETASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
143E3Ligand/Ion1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2EDO7Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
143E1Ligand/Ion1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
143E1Ligand/Ion1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
143E1Ligand/Ion1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:12 , TYR A:14 , ASP A:51 , HIS A:53 , GLY A:54 , MET A:227 , VAL A:229 , TRP A:230 , ASP A:232 , TYR A:237 , ILE A:265 , HOH A:826BINDING SITE FOR RESIDUE 43E A 601
02AC2SOFTWAREARG A:35 , ARG A:38BINDING SITE FOR RESIDUE EDO A 602
03AC3SOFTWAREILE B:12 , TYR B:14 , ASP B:51 , HIS B:53 , GLY B:54 , PHE B:213 , MET B:227 , TYR B:228 , VAL B:229 , TRP B:230 , ASP B:232 , ALA B:233 , TYR B:237 , ILE B:265 , HIS B:269 , HOH B:706 , HOH B:776 , HOH B:922BINDING SITE FOR RESIDUE 43E B 601
04AC4SOFTWAREARG B:35 , ARG B:38 , HOH B:936BINDING SITE FOR RESIDUE EDO B 602
05AC5SOFTWAREPRO B:68 , ARG B:69 , TRP B:215BINDING SITE FOR RESIDUE EDO B 603
06AC6SOFTWARELEU B:320 , ASP B:321 , GLN B:322 , GLN B:466BINDING SITE FOR RESIDUE EDO B 604
07AC7SOFTWAREARG B:80 , GLU B:84 , ASN B:90 , HOH B:795 , HOH B:903BINDING SITE FOR RESIDUE EDO B 605
08AC8SOFTWAREILE C:12 , TYR C:14 , ASP C:51 , HIS C:53 , GLY C:54 , MET C:227 , TYR C:228 , VAL C:229 , TRP C:230 , ASP C:232 , TYR C:237 , HIS C:269 , HOH C:733BINDING SITE FOR RESIDUE 43E C 601
09AC9SOFTWARETHR C:67 , PRO C:68 , ARG C:69 , HOH C:743BINDING SITE FOR RESIDUE EDO C 602
10BC1SOFTWARETYR C:119 , GLY C:121 , GLY C:122 , PHE C:165 , HOH C:752BINDING SITE FOR RESIDUE EDO C 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PY2)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Met A:187 -Pro A:188
2Tyr A:243 -Pro A:244
3Trp A:254 -Pro A:255
4Met B:187 -Pro B:188
5Tyr B:243 -Pro B:244
6Trp B:254 -Pro B:255
7Met C:187 -Pro C:188
8Tyr C:243 -Pro C:244
9Trp C:254 -Pro C:255

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PY2)

(-) Exons   (0, 0)

(no "Exon" information available for 4PY2)

(-) 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:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhhhhee.....ee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.ee.......ee..eeeeeehhhhhhhhhhhhh.......hhhhhhh...eeeee..hhhhhhhhhhhhhhhh.......eeee..eee..hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py2 A   3 REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGPQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNRIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY 508
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292    || 313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503     
                                                                                                                                                                                                                                                                                                                                297|                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                 309                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:487
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee.............eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.ee.......ee..eeeeeehhhhhhhhhhhhh.......hhhhhhh...eeeee..hhhhhhhhhhhhhhhh.......eeee..ee.hhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py2 B   3 REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEERYGPQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRYVE 510
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      |150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    || 313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       
                                                                                                                                                                  139|                                                                                                                                                295|                                                                                                                                                                                                         
                                                                                                                                                                   148                                                                                                                                                 309                                                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhhhhee.....ee.......eeeeeeeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.ee.......ee..eeeeeehhhhhhhhhhhhh.......hhhhhhh...eeeee..hhhhhhhhhhhhhhhh.......eeee..eee..hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py2 C   3 REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGPQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNRIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY 508
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292    || 313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503     
                                                                                                                                                                                                                                                                                                                                297|                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                 309
   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 4PY2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PY2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PY2)

(-) Gene Ontology  (9, 9)

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 Related Entries

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

UniProtKB/TrEMBL
        Q2YQ76_BRUA2 | Q2YQ76: 4dlp

(-) Related Entries Specified in the PDB File

4dlp SAME STRUCTURE WITH SEMET
4lne SAME STRUCTURE WITH CHEM 1312
4ppw SAME STRUCTURE WITH CHEM 1415 RELATED ID: SSGCID-BRABA.10201.A RELATED DB: TARGETTRACK