Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-160 V130D IN ACYL-ENZYME COMPLEX WITH AZTREONAM
 
Authors :  J. R. Clasman, C. M. June, R. A. Powers, D. A. Leonard
Date :  04 Dec 14  (Deposition) - 11 Mar 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Carbapenemase, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Mitchell, J. R. Clasman, C. M. June, K. C. Kaitany, J. R. Lafleur, M. A. Taracila, N. V. Klinger, R. A. Bonomo, T. Wymore, A. Szarecka, R. A. Powers, D. A. Leonard
Structural Basis Of Activity Against Aztreonam And Extended Spectrum Cephalosporins For Two Carbapenem-Hydrolyzing Clas D Beta-Lactamases From Acinetobacter Baumannii.
Biochemistry V. 54 1976 2015
PubMed-ID: 25710192  |  Reference-DOI: 10.1021/BI501547K

(-) Compounds

Molecule 1 - CLASS D BETA-LACTAMASE OXA-160
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 24A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BLAOXA-160
    Mutation: YES
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1AZR1Ligand/Ion2-({[(1Z)-1-(2-AMINO-1,3-THIAZOL-4-YL)-2-OXO-2-{[(2S,3S)-1-OXO-3-(SULFOAMINO)BUTAN-2-YL]AMINO}ETHYLIDENE]AMINO}OXY)-2-METHYLPROPANOIC ACID
2BCT1Ligand/IonBICARBONATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:80 , SER A:81 , SER A:128 , TRP A:167 , LYS A:218 , SER A:219 , GLY A:220 , TRP A:221 , GLY A:222 , MET A:223 , ARG A:261 , HOH A:487binding site for residue AZR A 301
2AC2SOFTWAREASN A:181 , HOH A:433binding site for residue BCT A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X53)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:170 -Pro A:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X53)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X53)

(-) Exons   (0, 0)

(no "Exon" information available for 4X53)

(-) 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:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeeee..eeeeee.hhhhhhh...hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x53 A  31 MHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSADPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTSQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
                                    40        50        60        70        80        90       100       110       120       130       140       150       160      |172       182       192       202       212       222       232       242       252       262       272   
                                                                                                                                                                  167|                                                                                                         
                                                                                                                                                                   170
   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 4X53)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X53)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X53)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AZR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BCT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:170 - Pro A:171   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4x53
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  D2XKK9_ACIBA | D2XKK9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  D2XKK9_ACIBA | D2XKK9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D2XKK9_ACIBA | D2XKK9: 4x56

(-) Related Entries Specified in the PDB File

4x55 4x56