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(-) Description

Title :  CRYSTAL STRUCTURE OF METHIONYL-TRNA SYNTHETASE METRS FROM BRUCELLA MELITENSIS IN COMPLEX WITH INHIBITOR CHEM 1415
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  17 May 16  (Deposition) - 25 May 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ssgcid, Metrs, Methionyl-Trna Synthetase, Brucella Melitensis, Protein Biosynthesis, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ligase (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 Plasmid: BRABA.10201.A.A1METG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BRABA.10201.A.A1
    Gene: METG, BR0995, BS1330_I0991
    Organism Scientific: BRUCELLA SUIS BIOVAR 1 (STRAIN 1330)
    Organism Taxid: 204722
    Strain: 1330
    Synonym: METHIONYL-TRNA SYNTHETASE,METRS

 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, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
14153Ligand/Ion1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2EDO8Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
14151Ligand/Ion1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
14151Ligand/Ion1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
14151Ligand/Ion1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-PHENYLUREA
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:12 , TYR A:14 , ASP A:51 , HIS A:53 , GLY A:54 , MET A:227 , TYR A:228 , VAL A:229 , TRP A:230 , TYR A:237 , PHE A:268 , HIS A:269binding site for residue 415 A 601
02AC2SOFTWARELYS A:18 , PRO A:19 , HIS A:20 , ILE A:309binding site for residue EDO A 602
03AC3SOFTWAREASP A:70 , PHE B:295binding site for residue EDO A 603
04AC4SOFTWAREGLU A:330binding site for residue EDO A 604
05AC5SOFTWAREASP A:73 , SER A:77 , ARG A:80 , ARG A:95binding site for residue EDO A 605
06AC6SOFTWAREILE 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 , LEU B:234 , TYR B:237 , ILE B:265 , PHE B:268 , HIS B:269binding site for residue 415 B 601
07AC7SOFTWAREGLY B:17 , HIS B:20 , GLU C:510binding site for residue EDO B 602
08AC8SOFTWAREASP B:390 , ASP B:393 , ALA B:394binding site for residue EDO B 603
09AC9SOFTWAREASP B:404 , ASP B:405binding site for residue EDO B 604
10AD1SOFTWAREALA C:11 , ILE C:12 , TYR C:14 , ASP C:51 , HIS C:53 , GLY C:54 , MET C:227 , VAL C:229 , TRP C:230 , ASP C:232 , ALA C:233 , LEU C:234 , TYR C:237 , PHE C:268 , HIS C:269binding site for residue 415 C 601
11AD2SOFTWAREGLU C:64binding site for residue EDO C 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K0T)

(-) 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 5K0T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K0T)

(-) Exons   (0, 0)

(no "Exon" information available for 5K0T)

(-) 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:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeee..eeee....eeehhhhhee.....ee.......eee..eeeee.hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhh....ee.ee.......ee..eeeeeehhhhhhhhhhhhh.......hhhhhhh...eeeee..hhhhhhhhhhhhhhhh.......eeee..eee..hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k0t A   2 SREKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGPQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNRIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY 508
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     ||312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502      
                                                                                                                                                                                                                                                                                                                                 297|                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                  309                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeee.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
                 5k0t B   2 SREKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRYVE 510
                                    11        21        31        41        51        61        71        81        91       101       111       121      |159       169       179       189       199       209       219       229       239       249       259       269       279       289     ||312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502        
                                                                                                                                                        128|                                                                                                                                       295|                                                                                                                                                                                                         
                                                                                                                                                         157                                                                                                                                        309                                                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:481
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeee............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
                 5k0t C   1 MSREKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHYKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYQGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSGLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWAYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNIDPFELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRSLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALGAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPFIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRYVE 510
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  157       167       177       187       197       207       217       227       237       247       257       267       277       287       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509 
                                                                                                                                                               134|                                                                                                                                             296|                                                                                                                                                                                                         
                                                                                                                                                                152                                                                                                                                              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 5K0T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K0T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K0T)

(-) Gene Ontology  (9, 9)

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