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 :  VIM-2 METALLO-BETA-LACTAMASE IN COMPLEX WITH 2-(3-FLUORO-4-HYDROXYPHENYL)-3-OXOISOINDOLINE-4-CARBOXYLIC ACID (COMPOUND 35)
 
Authors :  G. -B. Li, J. Brem, H. Someya, M. A. Mcdonough, C. J. Schofield
Date :  29 Jul 16  (Deposition) - 15 Feb 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.17
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Metallo-Beta-Lactamase, Inhibitor, Complex, Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. B. Li, M. I. Abboud, J. Brem, H. Someya, C. T. Lohans, S. Y. Yang, J. Spencer, D. W. Wareham, M. A. Mcdonough, C. J. Schofield
Nmr-Filtered Virtual Screening Leads To Non-Metal Chelating Metallo-Beta-Lactamase Inhibitors.
Chem Sci V. 8 928 2017
PubMed-ID: 28451231  |  Reference-DOI: 10.1039/C6SC04524C

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE VIM-2
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: OPINF VECTOR BASED ON PTRIEX VECTOR
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Gene: BLAVIM-2, BLA VIM-2, BLA-VIM-2, BLASVIM-2, BLAVIM2, BLM, VIM- 2, VIM-2, PAERUG_P32_LONDON_17_VIM_2_10_11_06255
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Other Details: 2-(3-FLUORO-4-HYDROXYPHENYL)-3-OXOISOINDOLINE-4- CARBOXYLIC ACID
    Synonym: BETA-LACTAMASE VIM-2,CLASS B BETA-LACTAMASE,CLASS B CARBAPENEMASE VIM-2,METALLO BETA LACTAMASE VIM-2,METALLO BETA- LACTAMASE,METALLO-BETA-LACTAMASE VIM-2,VIM-2,VIM-2 BETA-LACTAMASE, VIM-2 PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2H321Ligand/Ion2-(3-FLUORANYL-4-OXIDANYL-PHENYL)-3-OXIDANYLIDENE-1~{H}-ISOINDOLE-4-CARBOXYLIC ACID
3ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2H32-1Ligand/Ion2-(3-FLUORANYL-4-OXIDANYL-PHENYL)-3-OXIDANYLIDENE-1~{H}-ISOINDOLE-4-CARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2H321Ligand/Ion2-(3-FLUORANYL-4-OXIDANYL-PHENYL)-3-OXIDANYLIDENE-1~{H}-ISOINDOLE-4-CARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:114 , HIS B:116 , HIS B:179 , HOH B:632binding site for residue ZN B 501
02AC2SOFTWAREASP B:118 , ARG B:119 , CYS B:198 , HIS B:240 , HOH B:632 , HOH B:774binding site for residue ZN B 502
03AC3SOFTWAREHIS B:251 , FMT B:504 , FMT B:505binding site for residue ZN B 503
04AC4SOFTWAREHIS B:251 , ASN B:254 , ZN B:503 , FMT B:505binding site for residue FMT B 504
05AC5SOFTWAREHIS B:251 , ZN B:503 , FMT B:504 , HOH B:629binding site for residue FMT B 505
06AC6SOFTWAREHIS A:114 , HIS A:116 , HIS A:179 , ZN A:502 , HOH A:696binding site for residue ZN A 501
07AC7SOFTWAREASP A:118 , ARG A:119 , CYS A:198 , HIS A:240 , ZN A:501 , HOH A:602 , HOH A:696binding site for residue ZN A 502
08AC8SOFTWAREHIS A:153 , HIS A:251 , FMT A:505 , FMT A:506binding site for residue ZN A 503
09AC9SOFTWARETYR A:67 , TRP A:87 , HIS A:116 , ASP A:117 , ASP A:118 , HIS A:179 , GLY A:209 , ASN A:210 , HIS A:240 , HOH A:602 , HOH A:604 , HOH A:615 , HOH A:683 , HOH A:692binding site for residue H32 A 504
10AD1SOFTWAREALA A:132 , HIS A:153 , HIS A:251 , ASN A:254 , ZN A:503 , FMT A:506 , HOH A:631binding site for residue FMT A 505
11AD2SOFTWAREALA A:132 , THR A:152 , HIS A:153 , HIS A:251 , ZN A:503 , FMT A:505 , HOH A:632binding site for residue FMT A 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LM6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LM6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LM6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LM6)

(-) Exons   (0, 0)

(no "Exon" information available for 5LM6)

(-) 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:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee.........eeee..eeee...........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lm6 A  32 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR 262
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 


Chain B from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee........eeeee..eeeee..........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lm6 B  32 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR 262
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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  (0, 0)

(no "SCOP Domain" information available for 5LM6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LM6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LM6)

(-) Gene Ontology  (2, 2)

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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    H32  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5lm6)
 
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
  5lm6
    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
  Q9K2N0_PSEAI | Q9K2N0
    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
  Q9K2N0_PSEAI | Q9K2N0
    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
        Q9K2N0_PSEAI | Q9K2N0: 5k48 5n4s 5n4t 5nhz 5ni0
UniProtKB/TrEMBL
        Q9K2N0_PSEAI | Q9K2N0: 1ko2 1ko3 4bz3 4c1d 4c1e 4nq2 4pvo 4pvt 4ua4 5acu 5acv 5acw 5acx 5fqc 5lca 5lcf 5lch 5le1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LM6)