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(-) Description

Title :  CRYSTAL STRUCTURE OF OP0595 COMPLEXED WITH AMPC
 
Authors :  M. Yamada, T. Watanabe
Date :  07 Dec 14  (Deposition) - 01 Jul 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Morinaka, Y. Tsutsumi, M. Yamada, K. Suzuki, T. Watanabe, T. Abe, T. Furuuchi, S. Inamura, Y. Sakamaki, N. Mitsuhashi, T. Ida, D. M. Livermore
Op0595, A New Diazabicyclooctane: Mode Of Action As A Serin Beta-Lactamase Inhibitor, Antibiotic And Beta-Lactam 'Enhancer'
J. Antimicrob. Chemother. V. 70 2779 2015
PubMed-ID: 26089439  |  Reference-DOI: 10.1093/JAC/DKV166

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 32-387
    Gene: AMPC, PA4110
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228
    Synonym: CEPHALOSPORINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION
2OP02Ligand/Ion(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:90 , GLN A:146 , TYR A:177 , ASN A:179 , TYR A:249 , LYS A:342 , THR A:343 , GLY A:344 , SER A:345 , ASN A:373 , HOH A:572 , HOH A:605 , HOH A:620 , HOH A:621binding site for residue OP0 A 401
2AC2SOFTWAREHIS A:267 , ASP A:360binding site for residue NI A 402
3AC3SOFTWAREASP A:149 , HIS B:267 , ASP B:360binding site for residue NI A 403
4AC4SOFTWAREILE B:88 , GLY B:89 , VAL B:91 , SER B:92 , LYS B:93 , GLN B:146 , TYR B:177 , ASN B:179 , GLY B:248 , TYR B:249 , LYS B:342 , THR B:343 , GLY B:344 , SER B:345 , ASN B:373 , HOH B:668 , HOH B:713 , HOH B:714binding site for Di-peptide OP0 B 401 and SER B 90

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X68)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:303 -Pro A:304
2Trp B:303 -Pro B:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X68)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X68)

(-) Exons   (0, 0)

(no "Exon" information available for 4X68)

(-) 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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee..............eee...hhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhh.hhhhhhh................hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....ee...hhhhhhhh..ee.....ee......hhhhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eee....eeee...hhhhhhhhhhhhhhhh.ee.eeeeeeee....eeeeeeeee..eeeeeeeehhh.eeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x68 A  31 MDRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGL 387
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       


Chain B from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee..............eee...hhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhh.hhhhhhh................hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhh..ee.....ee......hhhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eee....eeee...hhhhhhhhhhhhhhhh.ee.eeeeeeee....eeeeeeee....eeeeeeehhh.eeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x68 B  31 MDRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGL 387
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380
   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 4X68)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X68)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X68)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  4x68
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  AMPC_PSEAE | P24735
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  3.5.2.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPC_PSEAE | P24735: 2wzx 2wzz 3s1y 3s22 4gzb 4hef 4nk3 4ooy 4wyy 4wz4

(-) Related Entries Specified in the PDB File

4x69