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 :  ACINETOBACTER BAUMANII OXA-24 COMPLEX WITH AVIBACTAM
 
Authors :  S. Mangani, M. Benvenuti, J. -D. Docquier
Date :  08 Oct 14  (Deposition) - 03 Dec 14  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Lactamase, Class D Carbapenemase, Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Lahiri, S. Mangani, H. Jahic, M. Benvenuti, T. F. Durand-Reville F. De Luca, D. E. Ehmann, G. M. Rossolini, R. A. Alm, J. D. Docquier
Molecular Basis Of Selective Inhibition And Slow Reversibility Of Avibactam Against Class D Carbapenemases: Structure-Guided Study Of Oxa-24 And Oxa-48.
Acs Chem. Biol. V. 10 591 2015
PubMed-ID: 25406838  |  Reference-DOI: 10.1021/CB500703P

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CO21Ligand/IonCARBON DIOXIDE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3NXL1Ligand/Ion(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE
4SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:80 , SER A:81 , TRP A:115 , SER A:128 , VAL A:130 , LEU A:168 , LYS A:218 , SER A:219 , GLY A:220 , TRP A:221 , MET A:223 , ARG A:261 , HOH A:459 , HOH A:481binding site for residue NXL A 301
2AC2SOFTWAREGLY A:141 , LEU A:142 , GLU A:143 , HOH A:455binding site for residue SO4 A 302
3AC3SOFTWARESER A:257 , GLY A:258 , SER A:259binding site for residue EDO A 303
4AC4SOFTWARELYS A:194 , LEU A:195 , GLU A:196binding site for residue EDO A 304
5AC5SOFTWARETHR A:99 , THR A:120 , LEU A:121 , GLY A:122 , MET A:204 , HOH A:439 , HOH A:469 , HOH A:476binding site for residue EDO A 305
6AC6SOFTWAREGLU A:39 , LYS A:43 , TYR A:66 , GLY A:67 , LEU A:70binding site for residue EDO A 306
7AC7SOFTWAREASN A:153 , PHE A:154 , GLY A:155 , GLN A:178 , ASN A:181 , PHE A:182 , HOH A:421binding site for residue EDO A 307
8AC8SOFTWARELYS A:84 , ASN A:87 , TRP A:167 , HOH A:481binding site for residue CO2 A 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WM9)

(-) 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 4WM9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WM9)

(-) Exons   (0, 0)

(no "Exon" information available for 4WM9)

(-) 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.....hhhhhhhhhhh.eeeee..eeeeeeeee....eeeeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wm9 A  31 FHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   ||  232       242       252       262       272   
                                                                                                                                                                                                                           224|                                                
                                                                                                                                                                                                                            227
   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 4WM9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WM9)

(-) 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
    CO2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NXL  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ 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
  4wm9
    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)
  (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
  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 5tg4 5tg5 5tg6 5tg7

(-) Related Entries Specified in the PDB File

2jc7 CONTAINS THE NATIVE PROTEIN