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(-) Description

Title :  CRYSTAL STRUCTURE OF ANT(2")-IA IN COMPLEX WITH AMPCPP AND GENTAMICIN C1
 
Authors :  D. Rodionov, A. V. Bassenden, A. M. Berghuis
Date :  08 Jul 15  (Deposition) - 16 Mar 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Antibiotic Resistance, Nucleotidyltransferase, Ampcpp, Gentamicin, Rossmann Fold, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. V. Bassenden, D. Rodionov, K. Shi, A. M. Berghuis
Structural Analysis Of The Tobramycin And Gentamicin Clinical Resistome Reveals Limitations For Next-Generation Aminoglycoside Design.
Acs Chem. Biol. V. 11 1339 2016
PubMed-ID: 26900880  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B01070

(-) Compounds

Molecule 1 - AMINOGLYCOSIDE NUCLEOTIDYLTRANSFERASE (2")-IA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AADB, TNCP6
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: AADB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
151G1Ligand/IonGENTAMICIN C1
2APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
3MN2Ligand/IonMANGANESE (II) ION
4P6G1Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:44 , ASP A:46 , MN A:202 , APC A:203 , HOH A:334binding site for residue MN A 201
2AC2SOFTWAREASP A:44 , ASP A:46 , ASP A:86 , MN A:201 , APC A:203 , 51G A:204binding site for residue MN A 202
3AC3SOFTWAREGLY A:28 , ARG A:40 , HIS A:42 , ASP A:43 , ASP A:44 , ASP A:46 , ASP A:131 , TYR A:132 , TYR A:135 , HIS A:148 , MN A:201 , MN A:202 , 51G A:204 , HOH A:307 , HOH A:308 , HOH A:334 , HOH A:342 , HOH A:361 , HOH A:371 , HOH A:377 , HOH A:383 , HOH A:405binding site for residue APC A 203
4AC4SOFTWAREASP A:46 , TYR A:74 , LEU A:77 , ASP A:86 , GLU A:88 , ILE A:99 , ALA A:100 , ASP A:131 , TYR A:134 , MN A:202 , APC A:203 , HOH A:361 , HOH A:383 , HOH A:385 , HOH A:398 , HOH A:418 , HOH A:441binding site for residue 51G A 204
5AC5SOFTWARETHR A:7 , LYS A:11 , ARG A:34 , LEU A:35 , GLY A:36 , LEU A:64 , ALA A:111 , GLU A:112 , VAL A:114 , PRO A:119 , HOH A:365binding site for residue P6G A 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CFT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CFT)

(-) 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:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....eehhhhhhhhhhh........eeeeee..hhhhhhhhhhhh..eeeee....eeeee..eeeeeeeeeee..eee..............eee..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cft A   2 DTTQVTLIHKILAAADERNLPLWIGGGWAIDARLGRVTRKHDDIDLTFPGERRGELEAIVEMLGGRVMEELDYGFLAEIGDELLDCEPAWWADEAYEIAEAPQGSCPEAAEGVIAGRPVRCNSWEAIIWDYFYYADEVPPVDWPTKHIESYRLACTSLGAEKVEVLRAAFRSRYA 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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 5CFT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5CFT)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        Q6X3H6_PSEAI | Q6X3H6: 4xje 5cfs 5cfu

(-) Related Entries Specified in the PDB File

4xje 4XJE CONTAINS THE SAME PROTEIN IN COMPLEX WITH TOBRAMYCIN AND AMP
5cfs
5cfu