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 :  MUTAGENESIS OF ZINC LIGAND RESIDUE CYS221 REVEALS PLASTICITY IN THE IMP-1 METALLO-B-LACTAMASE ACTIVE SITE
 
Authors :  L. B. Horton, S. Shanker, R. Mikulski, N. G. Brown, K. Phillips, E. Lykis B. V. V. Prasad, T. G. Palzkill
Date :  14 May 12  (Deposition) - 27 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Metallo-B-Lactamase, B-Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. B. Horton, S. Shanker, R. Mikulski, N. G. Brown, K. J. Phillips, E. Lykissa, B. V. Venkataram Prasad, T. Palzkill
Mutagenesis Of Zinc Ligand Residue Cys221 Reveals Plasticit In The Imp-1 Metallo-Beta-Lactamase Active Site
Antimicrob. Agents Chemother. V. 56 5667 2012
PubMed-ID: 22908171  |  Reference-DOI: 10.1128/AAC.01276-12

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BLAIMP-1, BLA IMP, BLA-IMP, BLAESP, IMP
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: BETA-LACTAMASE IMP-1, BLA-IMP PROTEIN, EXTENDED-SPECTRUM B- LACTAMASE, IMP-1 METALLO-BETA-LACTMASE, METALLO BETA LACTAMASE, METALLO-BETA-LACTAMASE, METALLO-BETA-LACTAMASE IMP-1, METALLO-BETA- LACTAMASE BLAIMP-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2SO42Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:77 , HIS A:79 , HIS A:139 , SO4 A:304BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREILE A:160 , LYS A:161 , PRO A:162 , SER A:196 , HIS A:197 , SER A:198 , HOH A:535BINDING SITE FOR RESIDUE PO4 A 302
3AC3SOFTWARETRP A:124 , GLU A:131 , LYS A:186 , HOH A:514 , HOH A:542BINDING SITE FOR RESIDUE PO4 A 303
4AC4SOFTWAREHIS A:77 , HIS A:79 , ASP A:81 , HIS A:139 , LYS A:161 , SER A:196 , HIS A:197 , ZN A:301BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWARELYS A:11 , TYR A:17 , TRP A:28 , GLN A:233 , PHE A:234 , GLU A:235 , HOH A:504 , HOH A:545 , HOH A:547BINDING SITE FOR RESIDUE SO4 A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F6H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F6H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F6H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F6H)

(-) Exons   (0, 0)

(no "Exon" information available for 4F6H)

(-) 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:223
                                                                                                                                                                                                                                                               
               SCOP domains d4f6ha_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f6h A   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGGFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESHPQFEK 236
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      |233   
                                                                                                                                                                                                                                                  220|     
                                                                                                                                                                                                                                                   231
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F6H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F6H)

(-) Gene Ontology  (6, 6)

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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4f6h)
 

(-) 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
  4f6h
    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
  Q79MP6_PSEAI | Q79MP6
    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
  Q79MP6_PSEAI | Q79MP6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q79MP6_PSEAI | Q79MP6: 1ddk 1jje 1jjt 3wxc 4f6z

(-) Related Entries Specified in the PDB File

4f6z