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 OXA-1 CLASS D BETA-LACTAMASE
 
Authors :  T. Sun, M. Nukaga, K. Mayama, E. H. Braswell, J. R. Knox
Date :  16 Jul 02  (Deposition) - 14 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Side Chain Modification, Lysine Carbamylation, Hydrolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sun, M. Nukaga, K. Mayama, E. H. Braswell, J. R. Knox
Comparison Of Beta-Lactamases Of Classes A And D: 1. 5A Crystallographic Structure Of The Class D Oxa-1 Oxacillinase
Protein Sci. V. 12 82 2003
PubMed-ID: 12493831  |  Reference-DOI: 10.1110/PS.0224303
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE OXA-1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET12A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: OXA1
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PENICILLINASE, OXACILLINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2MPD10Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:117 , ALA A:215 , HOH A:502 , HOH A:934 , SER B:237BINDING SITE FOR RESIDUE MPD A 401
02AC2SOFTWARESER A:237 , VAL B:117 , ALA B:215 , HOH B:503 , HOH B:877BINDING SITE FOR RESIDUE MPD B 402
03AC3SOFTWAREILE A:82 , PHE A:90 , GLU A:122 , LYS A:126 , HOH A:894 , HOH A:974 , HOH B:762BINDING SITE FOR RESIDUE MPD A 403
04AC4SOFTWAREGLU B:122 , HOH B:956BINDING SITE FOR RESIDUE MPD B 404
05AC5SOFTWAREPHE A:114 , GLY A:142 , ASN A:143 , HOH A:701BINDING SITE FOR RESIDUE MPD A 405
06AC6SOFTWAREASN A:193 , LEU B:251BINDING SITE FOR RESIDUE MPD A 406
07AC7SOFTWAREPHE B:114 , GLY B:142 , ASN B:143 , HOH B:768BINDING SITE FOR RESIDUE MPD B 407
08AC8SOFTWAREASN A:183 , LEU A:184 , PRO A:185 , ARG B:222BINDING SITE FOR RESIDUE MPD A 408
09AC9SOFTWARELYS A:187 , ASN A:188 , HOH A:683 , HOH A:717BINDING SITE FOR RESIDUE MPD A 409
10BC1SOFTWARELYS A:236 , SER A:237 , HOH A:710 , VAL B:117 , GLN B:121 , GLU B:158 , LEU B:161 , HOH B:787BINDING SITE FOR RESIDUE MPD B 410

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:37 -A:59
2B:37 -B:59

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M6K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M6K)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO1_ECOLX69-79
 		  2A:65-75
B:65-75

(-) Exons   (0, 0)

(no "Exon" information available for 1M6K)

(-) 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:250
 aligned with BLO1_ECOLX | P13661 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:251
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 
           BLO1_ECOLX    26 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 276
               SCOP domains d1m6ka_ A: Class D beta-lactamase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1m6kA00 A:18-274 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh..eeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh.........-...hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhh.eeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m6k A  18 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFkIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGD-ERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    27  ||    39   ||   51        61        71        81 ||     92       102       112       122       132       142      |152       162       172       182       192       202       212    || 223       233       243       253       263       273 
                                       30|        43|                      70-KCX       83|                                                             149 |                                                               217|                                                       
                                        33         46                                    85                                                               151                                                                219                                                       


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with BLO1_ECOLX | P13661 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:251
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 
           BLO1_ECOLX    26 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 276
               SCOP domains d1m6kb_ B: Class D beta-lactamase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1m6kB00 B:18-274 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                    CATH domains
           Pfam domains (1) ----------------Transpeptidase-1m6kB01 B:36-271                                                                                                                                                                                                         --- Pfam domains (1)
           Pfam domains (2) ----------------Transpeptidase-1m6kB02 B:36-271                                                                                                                                                                                                         --- Pfam domains (2)
         Sec.struct. author .eehhhhhhhhhh..eeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh.........-...hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhh.eeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m6k B  18 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFkIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGD-ERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    27  ||    39   ||   51        61        71        81 ||     92       102       112       122       132       142      |152       162       172       182       192       202       212    || 223       233       243       253       263       273 
                                       30|        43|                      70-KCX       83|                                                             149 |                                                               217|                                                       
                                        33         46                                    85                                                               151                                                                219
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLO1_ECOLX | P13661)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

 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
    KCX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1m6k)
 

(-) 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
  1m6k
    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
  BLO1_ECOLX | P13661
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  BLO1_ECOLX | P13661
    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
        BLO1_ECOLX | P13661: 3isg 4mll

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1M6K)