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(-) Description

Title :  EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH THIOMURACIN ANALOG
 
Authors :  D. Palestrant, T. Stams
Date :  13 Apr 16  (Deposition) - 13 Jul 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Natural Product Inhibitor, Elongation Factor, Rna Binding Protein- Antimicrobial Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Lamarche, J. A. Leeds, J. Brewer, K. Dean, J. Ding, J. Dzink-Fox, G. Gamber, A. Jain, R. Kerrigan, P. Krastel, K. Lee, F. Lombardo, D. Mckenney, G. Neckermann, C. Osborne, D. Palestrant, M. A. Patane, E. M. Rann, Z. Robinson, E. Schmitt, T. Stams, S. Tiamfook, D. Yu, L. Whitehead
Antibacterial And Solubility Optimization Of Thiomuracin A.
J. Med. Chem. V. 59 6920 2016
PubMed-ID: 27355833  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00726

(-) Compounds

Molecule 1 - ELONGATION FACTOR TU 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TUFA, B3339, JW3301
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: EF-TU 1,BACTERIOPHAGE Q BETA RNA-DIRECTED RNA POLYMERASE SUBUNIT III,P-43
 
Molecule 2 - THIOMURACIN ANALOG
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 14)

Asymmetric/Biological Unit (9, 14)
No.NameCountTypeFull Name
105N1Mod. Amino Acid(3R,4R)-4-HYDROXY-3-METHYL-L-PROLINE
26RK1Mod. Amino Acid4-AZANYLCYCLOHEXANE-1-CARBOXYLIC ACID
3BB61Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID
4BB95Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
5GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
6H141Mod. Amino Acid(2S,3R)-BETA-HYDROXY-PHENYLALANINE
7MG2Ligand/IonMAGNESIUM ION
8MH61Mod. Amino Acid3-HYDROXY-2-IMINOPROPANOIC ACID
9SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:21 , HIS A:22 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , PHE A:46 , ASN A:135 , LYS A:136 , ASP A:138 , MET A:139 , SER A:173 , ALA A:174 , LEU A:175 , MG A:403 , HOH A:576 , HOH A:578 , HOH A:603 , HOH A:627 , HOH A:654BINDING SITE FOR RESIDUE GDP A 401
2AC2SOFTWAREHOH A:510 , HOH A:554 , HOH A:636BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWARETHR A:25 , GDP A:401BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWAREARG A:262 , ARG A:318 , HIS A:319 , THR A:320 , ARG A:381BINDING SITE FOR RESIDUE SO4 A 404
5AC5SOFTWARETHR A:73 , ALA A:182 , GLU A:215 , ILE A:220 , ARG A:223 , THR A:228 , GLY A:257 , GLU A:259 , PHE A:261 , ARG A:262 , LEU A:264 , ASN A:273 , VAL A:274 , GLY A:275 , LEU A:277 , THR A:320 , PRO A:321 , PHE A:323 , LYS A:324 , GLY A:325 , HOH A:527 , HOH B:101 , HOH B:102 , HOH B:103 , HOH B:104 , HOH B:105 , HOH B:106BINDING SITE FOR CHAIN B OF THIOMURACIN ANALOG

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:379 -Gly A:380

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JBQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JBQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhh..eee....eee.eeeeee....eeeeee..hhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhhhh..hhhhh.eee.hhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhh..eee...eeee...eeeeeee....eee...eeeee.....eeeeeeeeee..eee.eee...eeeeee...hhhhh....eee.....eeeeeeeeeeee...........ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeeee....eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jbq A   2 KEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG 393
                                    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       301       311       321       331       341       351       361       371       381       391  


Chain B from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5jbq B   1 SxNxxxYxxxxxx  13
                             | ||| |10|||
                             2-BB9 ||||13-6RK
                               4-BB6|||| 
                                5-H14||| 
                                 6-BB9|| 
                                   8-05N 
                                    9-BB9
                                    10-BB9
                                     11-MH6
                                      12-BB9
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5JBQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:379 - Gly A:380   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        EFTU1_ECOLI | P0CE47: 1d8t 1dg1 1efc 1efm 1efu 1etu 1ls2 1mj1 1qzd 2bvn 2fx3 2hcj 2hdn 3ep2 3eq3 3eq4 3u2q 3u6b 3u6k 4g5g 4pc3 4pc7 4q7j 4v69

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