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

(-) Description

Title :  METALLO-BETA-LACTAMASE WITH MES
 
Authors :  P. M. D. Fitzgerald, J. K. Wu, J. H. Toney
Date :  17 Mar 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Beta-Lactamase), Metallo Beta-Lactamase, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. M. Fitzgerald, J. K. Wu, J. H. Toney
Unanticipated Inhibition Of The Metallo-Beta-Lactamase From Bacteroides Fragilis By 4-Morpholineethanesulfonic Acid (Mes): A Crystallographic Study At 1. 85-A Resolution.
Biochemistry V. 37 6791 1998
PubMed-ID: 9578564  |  Reference-DOI: 10.1021/BI9730339
(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
    Expression System Taxid: 562
    Gene: CCRA
    Mutation: YES
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 817
    Strain: TAL3636
    Synonym: CLASS B BETA-LACTAMASE
    Variant: CLINICAL ISOLATE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2NA2Ligand/IonSODIUM ION
3ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:82 , HIS A:84 , HIS A:145 , ZN A:252 , HOH A:256BINDING SITE FOR RESIDUE ZN A 251
2AC2SOFTWAREASP A:86 , CYS A:164 , HIS A:206 , ZN A:251 , HOH A:256 , HOH A:257BINDING SITE FOR RESIDUE ZN A 252
3AC3SOFTWAREASN A:38 , ASP A:52 , ASP A:86 , HOH A:258 , HOH A:266BINDING SITE FOR RESIDUE NA A 255
4AC4SOFTWAREHIS B:82 , HIS B:84 , HIS B:145 , ZN B:252 , HOH B:256BINDING SITE FOR RESIDUE ZN B 251
5AC5SOFTWAREASP B:86 , CYS B:164 , HIS B:206 , ZN B:251 , HOH B:256 , HOH B:257BINDING SITE FOR RESIDUE ZN B 252
6AC6SOFTWAREASN B:38 , ASP B:52 , ASP B:86 , HOH B:259 , HOH B:263BINDING SITE FOR RESIDUE NA B 255
7AC7SOFTWARETRP A:32 , ASP A:86 , HIS A:145 , GLY A:175 , ASN A:176 , HIS A:206 , HOH A:257 , HOH A:329 , ARG B:200BINDING SITE FOR RESIDUE MES A 250
8AC8SOFTWARETRP B:32 , ASP B:86 , HIS B:145 , GLY B:175 , ASN B:176 , HOH B:257 , HOH B:282 , HOH B:342BINDING SITE FOR RESIDUE MES B 250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A7T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A7T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A7T)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_BACFG96-115
 		  2A:79-98
B:79-98
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_BACFG172-184
 		  2A:155-167
B:155-167

(-) Exons   (0, 0)

(no "Exon" information available for 1A7T)

(-) 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:227
 aligned with BLAB_BACFG | P25910 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           BLAB_BACFG    21 SVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTS 247
               SCOP domains d1a7ta_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                SCOP domains
               CATH domains 1a7tA00 A:4-230 Metallo-beta-lactamase, chain A                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .......eeeee....eeeeeeeeee...eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhh..eeeeee.....hhhh..hhhhhh...eeeeehhhhhhhhhh......eee..eeeeee..eeeeee...........eeee....----hhh................hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------eeeee------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS--------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a7t A   4 SVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGNYGGTELIEHTKQIVNQYIESTS 230
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with BLAB_BACFG | P25910 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           BLAB_BACFG    21 SVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTS 247
               SCOP domains d1a7tb_ B: Zn metallo-beta-lactamase                                                                                                                                                                                                SCOP domains
               CATH domains 1a7tB00 B:4-230 Metallo-beta-lactamase, chain A                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .......eeeee....eeeeeeeeee...eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhh..eeeeee.....hhhh..hhhhhh...eeeeehhhhhhhhh.......eee..eeeeee..eeeeee...........eeee....----hhh................hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------eeeee------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS--------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a7t B   4 SVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGNYGGTELIEHTKQIVNQYIESTS 230
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A7T)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLAB_BACFG | P25910)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1a7t)
 

(-) 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
  1a7t
    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: 1a8t 1hlk 1kr3 1znb 2bmi 2znb 3znb 4znb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1A7T)