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 :  CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-2
 
Authors :  F. Kerff, E. Fonze, F. Bouillenne, J. M. Frere, P. Charlier
Date :  02 Oct 01  (Deposition) - 24 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine Beta-Lactamase, Hydrolase, Antibiotic Resistance, Carbamylated Lysine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Kerff, E. Fonze, F. Bouillenne, J. M. Frere, P. Charlier
Crystal Structure Of The Class D Beta-Lactamase Oxa-2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE OXA-2
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDML303
    Expression System Strain: JM105
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OXA-2
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: PENICILLINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:115 , THR A:206 , GLY A:207 , TRP A:208 , ARG A:244 , ASN B:96BINDING SITE FOR RESIDUE FMT A 401
2AC2SOFTWAREASN A:96 , SER B:115 , THR B:206 , TRP B:208 , ARG B:244BINDING SITE FOR RESIDUE FMT B 402
3AC3SOFTWAREHOH A:479 , PHE B:180 , ARG B:181 , HOH B:406 , HOH B:429 , HOH B:501BINDING SITE FOR RESIDUE FMT B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K38)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K38)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K38)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO2_SALTM70-80
 		  2A:65-75
B:65-75

(-) Exons   (0, 0)

(no "Exon" information available for 1K38)

(-) 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:239
 aligned with BLO2_SALTM | P0A1V8 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:241
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
           BLO2_SALTM    25 TLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPP 265
               SCOP domains d1k38a_ A: Class D beta-lactamase                                                                                                                                                                                                                 SCOP domains
               CATH domains 1k38A00 A:20-260 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhh...eeeeeee........eeehhhhhh....hhhhhhhhhhhhhhhh..........................hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.........--...........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k38 A  20 TLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFkIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPST--GDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPP 260
                                    29        39        49        59        69|       79        89        99       109       119       129       139        |- |     159       169       179       189       199       209       219       229       239       249       259 
                                                                             70-KCX                                                                       148  |                                                                                                             
                                                                                                                                                             151                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with BLO2_SALTM | P0A1V8 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:241
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
           BLO2_SALTM    25 TLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPP 265
               SCOP domains d1k38b_ B: Class D beta-lactamase                                                                                                                                                                                                                 SCOP domains
               CATH domains 1k38B00 B:20-260 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhh...eeeeeee........eeehhhhhh....hhhhhhhhhhhhhhhh..................---.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........---hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k38 B  20 TLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFkIPHTLFALDAGAVRDEFQIFRWDGVNRG---HNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPST---DYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPP 260
                                    29        39        49        59        69|       79        89        |-  |    109       119       129       139        |-  |    159       169       179       189       199       209       219       229       239       249       259 
                                                                             70-KCX                      98 102                                           148 152
   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  (0, 0)

(no "Pfam Domain" information available for 1K38)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLO2_SALTM | P0A1V8)
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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    KCX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k38)
 

(-) 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
  1k38
    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
  BLO2_SALTM | P0A1V8
    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
  BLO2_SALTM | P0A1V8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1K38)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1K38)