Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  METALLO-BETA-LACTAMASE (C181S MUTANT)
 
Authors :  Z. Li, O. Herzberg
Date :  20 Oct 98  (Deposition) - 08 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Beta-Lactamase, Metallo Beta-Lactamase, Cadmium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Li, B. A. Rasmussen, O. Herzberg
Structural Consequences Of The Active Site Substitution Cys181 --> Ser In Metallo-Beta-Lactamase From Bacteroides Fragilis.
Protein Sci. V. 8 249 1999
PubMed-ID: 10210203
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Gene: CCRA3 (WITHOUT SIGNAL SEQUENCE)
    Expression System Plasmid: PCLL2216
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CCRA3 (WITHOUT SIGNAL SEQUENCE
    Mutation: YES
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 817
    Synonym: CLASS B BETA-LACTAMASE
    Variant: CLINICAL ISOLATE QMCN3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:99 , HIS A:101 , ASP A:103 , HIS A:162 , HOH A:250BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREASN A:55 , ASP A:69 , ASP A:103 , HOH A:256BINDING SITE FOR RESIDUE NA A 3
3AC3SOFTWAREHIS B:99 , HIS B:101 , HIS B:162 , HOH B:250BINDING SITE FOR RESIDUE ZN B 1
4AC4SOFTWAREASN B:55 , ASP B:69 , ASP B:103 , HOH B:253BINDING SITE FOR RESIDUE NA B 3
5NAAUNKNOWNASN A:55 , ASP A:69 , ASP A:103 , HOH A:256DEDUCED FROM THE COORDINATION. SODIUM WAS PRESENT IN THE CRYSTALLIZATION SOLUTION.
6NABUNKNOWNASN B:55 , ASP B:69 , ASP B:103 , HOH B:253DEDUCED FROM THE COORDINATION. SODIUM WAS PRESENT IN THE CRYSTALLIZATION SOLUTION.
7ZNAUNKNOWNHIS A:99 , HIS A:101 , HIS A:162 , HOH A:250ONLY THE ZN1 SITE OF THE BINUCLEAR ZINC CENTER IS OCCUPIED.
8ZNBUNKNOWNHIS B:99 , HIS B:101 , HIS B:162 , HOH B:250ONLY THE ZN1 SITE OF THE BINUCLEAR ZINC CENTER IS OCCUPIED.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZNB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZNB)

(-) Sequences/Alignments

Asymmetric 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains d4znba_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                SCOP domains
               CATH domains 4znbA00 A:21-249 Metallo-beta-lactamase, chain A                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eee...eeeee....eeeeeeeee...eeeeeeeeeee..eeeee.....hhhhhhhhhhhhh....eeeeee.....hhhh..hhhhhhh..eeeeehhhhhhhhh.......eee..eeeeee..eeeeee...........eeeehhh.----hhh................hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhh... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------eeeee--------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4znb A  21 SVKISDDISITQLSDKVYTYVSLAEIEGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGSMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP 249
                                    30        40      ||52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
                                                     47|                                                                                                                                                                                                       
                                                      50                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains d4znbb_ B: Zn metallo-beta-lactamase                                                                                                                                                                                            SCOP domains
               CATH domains 4znbB00 B:21-247 Metallo-beta-lactamase, chain A                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeee..eeeee....eeeeeeee...eeeeeeeeee..eeeee.....hhhhhhhhhhhhh....eeeeee.....hhhh..hhhhhhh..eeeeehhhhhhhhh.......eee..eeeeee..eeeeeee.........eeeee....----hhh................hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------------------------------------------------------------------------------------------------------------------------------eeeee------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4znb B  21 SVKISDDISITQLSDKVYTYVSLAEIMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGSMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTS 247
                                    30        40     || 54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244   
                                                    46|                                                                                                                                                                                                    
                                                     51
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    NAA  [ RasMol ]  +environment [ RasMol ]
    NAB  [ RasMol ]  +environment [ RasMol ]
    ZNA  [ RasMol ]  +environment [ RasMol ]
    ZNB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4znb)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4znb
    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
  BLAB_BACFG | P25910
    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
  BLAB_BACFG | P25910
    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
        BLAB_BACFG | P25910: 1a7t 1a8t 1hlk 1kr3 1znb 2bmi 2znb 3znb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZNB)