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 :  OXA-24/40 IN COMPLEX WITH BORONIC ACID BA3
 
Authors :  R. A. Powers, J. P. Werner, J. M. Mitchell
Date :  27 Sep 16  (Deposition) - 11 Jan 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Complex, Lactamase, Oxa, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Werner, J. M. Mitchell, M. A. Taracila, R. A. Bonomo, R. A. Powers
Exploring The Potential Of Boronic Acids As Inhibitors Of Oxa-24/40 Beta-Lactamase.
Protein Sci. V. 26 515 2017
PubMed-ID: 27997706  |  Reference-DOI: 10.1002/PRO.3100

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24A
    Expression System Taxid: 469008
    Gene: BLAOXA-33, BLA-OXA-40, BLAOXA-24, BLAOXA-40, OXA-24, OXA40
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470
    Synonym: BETA-LACTAMASE OXA-33,BETALACTAMASE OXA24,CARBAPENEM- HYDROLYZING BETA-LACTAMASE OXA-40,CARBAPENEM-HYDROLYZING OXACILLINASE,CARBAPENEM-HYDROLYZING OXACILLINASE OXA-40,CARBAPENEMASE OXA-24,CLASS D BETA-LACTAMASE OXA-40,OXA24 B-LACTAMASE,OXA40

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric/Biological Unit (6, 7)
No.NameCountTypeFull Name
1ABA1Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2BCT1Ligand/IonBICARBONATE ION
3JW31Ligand/Ion(3-{[(FURAN-2-YL)METHYL]CARBAMOYL}PHENYL)BORONIC ACID
4KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5MEE1Ligand/IonMETHANETHIOL
6SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:80 , SER A:81 , TRP A:115 , SER A:128 , VAL A:130 , LEU A:168 , GLY A:220 , TRP A:221 , MET A:223 , SO4 A:302 , HOH A:412binding site for residue JW3 A 301
2AC2SOFTWARETYR A:112 , MET A:223 , JW3 A:301 , MEE A:304binding site for residue SO4 A 302
3AC3SOFTWAREGLY A:141 , GLU A:143binding site for residue SO4 A 303
4AC4SOFTWAREABA A:114 , LEU A:127 , SO4 A:302binding site for residue MEE A 304
5AC5SOFTWAREASN A:181binding site for residue BCT A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TG7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:170 -Pro A:171
2Thr A:226 -Pro A:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TG7)

(-) Exons   (0, 0)

(no "Exon" information available for 5TG7)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...eeeeeee..eeeeee.hhhhhhh...hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhh.eeeee..eeeeeeeee......eeeeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tg7 A  32 HISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFkMLNALIGLENHKATTNEIFKWDGKKRTYPxWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
                                    41        51        61        71        81  |     91       101       111  |    121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
                                                                               84-KCX                       114-ABA
   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 5TG7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TG7)

(-) Gene Ontology  (2, 2)

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
    ABA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BCT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    JW3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    KCX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MEE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:170 - Pro A:171   [ RasMol ]  
    Thr A:226 - Pro A:227   [ 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
  5tg7
    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
  Q8RLA6_ACIBA | Q8RLA6
    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)
  3.5.2.6
    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
  Q8RLA6_ACIBA | Q8RLA6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q8RLA6_ACIBA | Q8RLA6: 5vfd
UniProtKB/TrEMBL
        Q8RLA6_ACIBA | Q8RLA6: 2jc7 3fv7 3fyz 3fzc 3g4p 3mbz 3pae 3pag 3znt 4f94 4wm9 5tg4 5tg5 5tg6

(-) Related Entries Specified in the PDB File

5tg4 5tg5 5tg6