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 :  VIM-2-2, DISCOVERY OF NOVEL INHIBITOR SCAFFOLDS AGAINST THE METALLO-BETA-LACTAMASE VIM-2 BY SPR BASED FRAGMENT SCREENING
 
Authors :  T. Christopeit, T. J. O. Carlsen, R. Helland, H. K. S. Leiros
Date :  18 Aug 15  (Deposition) - 04 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Christopeit, T. J. O. Carlsen, R. Helland, H. K. S. Leiros
Discovery Of Novel Inhibitor Scaffolds Against The Metallo-Beta-Lactamase Vim-2 By Spr Based Fragment Screening
J. Med. Chem. V. 58 8671 2015
PubMed-ID: 26477515  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01289

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: 301-5473

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
3OH2Ligand/IonHYDROXIDE ION
4WL32Ligand/Ion2-(4-FLUOROPHENYL)CARBONYLBENZOIC ACID
5ZN6Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , OCS A:221 , ZN A:1002 , WL3 A:1298 , OH A:1299BINDING SITE FOR RESIDUE ZN A1001
02AC2SOFTWAREASP A:120 , OCS A:221 , HIS A:263 , ZN A:1001 , WL3 A:1298 , OH A:1299BINDING SITE FOR RESIDUE ZN A1002
03AC3SOFTWAREHIS A:170 , HIS A:285 , CL A:1300 , CL A:1301BINDING SITE FOR RESIDUE ZN A1003
04AC4SOFTWAREHIS B:116 , HIS B:118 , HIS B:196 , OCS B:221 , ZN B:1002 , WL3 B:1298 , OH B:1299BINDING SITE FOR RESIDUE ZN B1001
05AC5SOFTWAREASP B:120 , OCS B:221 , HIS B:263 , ZN B:1001 , WL3 B:1298 , OH B:1299BINDING SITE FOR RESIDUE ZN B1002
06AC6SOFTWAREHIS B:170 , HIS B:285 , CL B:1300 , CL B:1301BINDING SITE FOR RESIDUE ZN B1003
07AC7SOFTWARETYR B:67 , TRP B:87 , ASP B:119 , ASP B:120 , HIS B:196 , OCS B:221 , ARG B:228 , ASN B:233 , HIS B:263 , ZN B:1001 , ZN B:1002 , OH B:1299 , HOH B:2218 , HOH B:2231BINDING SITE FOR RESIDUE WL3 B1298
08AC8SOFTWARETYR A:67 , HIS A:118 , ASP A:119 , ASP A:120 , HIS A:196 , OCS A:221 , ASN A:233 , HIS A:263 , ZN A:1001 , ZN A:1002 , OH A:1299 , HOH A:2232 , HOH A:2243BINDING SITE FOR RESIDUE WL3 A1298
09AC9SOFTWAREHIS B:116 , HIS B:118 , ASP B:120 , HIS B:196 , OCS B:221 , ZN B:1001 , ZN B:1002 , WL3 B:1298BINDING SITE FOR RESIDUE OH B1299
10BC1SOFTWAREHIS A:116 , HIS A:118 , ASP A:120 , HIS A:196 , OCS A:221 , ZN A:1001 , ZN A:1002 , WL3 A:1298BINDING SITE FOR RESIDUE OH A1299
11BC2SOFTWAREHIS A:170 , HIS A:285 , ZN A:1003 , CL A:1301 , HOH A:2163 , HOH A:2257BINDING SITE FOR RESIDUE CL A1300
12BC3SOFTWAREALA A:135 , HIS A:170 , HIS A:285 , ASN A:288 , ZN A:1003 , CL A:1300 , HOH A:2306BINDING SITE FOR RESIDUE CL A1301
13BC4SOFTWAREHIS B:170 , HIS B:285 , ASN B:288 , ZN B:1003 , CL B:1301 , HOH B:2066BINDING SITE FOR RESIDUE CL B1300
14BC5SOFTWAREHIS B:170 , HIS B:285 , ZN B:1003 , CL B:1300 , HOH B:2152BINDING SITE FOR RESIDUE CL B1301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ACX)

(-) 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:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....eeeeeee..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
                 5acx A  29 GEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGcAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 297
                                    38      ||49        59    ||  70        80        90       100|    ||112       122       133       143      |167       177       187       197       210||     223       233       243       253       263 ||    284       294   
                                           45|               64|                               100|  107|                   131|              150|                                     205| ||     |                                         265|                    
                                            47                66                                102   109                    133               165                                      209 ||     |                                          277                    
                                                                                                                                                                                          211|     |                                                                 
                                                                                                                                                                                           215     |                                                                 
                                                                                                                                                                                                 221-OCS                                                             


Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....eeeeeee..eeeeeeeee....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee.........eeee..eeee...........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5acx B  29 GEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGcAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 297
                                    38      ||49        59    ||  70        80        90       100|    ||112       122       133       143      |167       177       187       197       210||     223       233       243       253       263 ||    284       294   
                                           45|               64|                               100|  107|                   131|              150|                                     205| ||     |                                         265|                    
                                            47                66                                102   109                    133               165                                      209 ||     |                                          277                    
                                                                                                                                                                                          211|     |                                                                 
                                                                                                                                                                                           215     |                                                                 
                                                                                                                                                                                                 221-OCS
   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 5ACX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OCS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    WL3  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5acx)
 

(-) 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
  5acx
    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)
  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
  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 5fqc 5lca 5lcf 5lch 5le1 5lm6

(-) Related Entries Specified in the PDB File

5acu VIM-2-NAT, DISCOVERY OF NOVEL INHIBITOR SCAFFOLDS AGAINST THE METALLO-BETA-LACTAMASE VIM-2 BY SPR BASED FRAGMENT SCREENING
5acv VIM-2-NAT, DISCOVERY OF NOVEL INHIBITOR SCAFFOLDS AGAINST THE METALLO-BETA-LACTAMASE VIM-2 BY SPR BASED FRAGMENT SCREENING
5acw VIM-2-1, DISCOVERY OF NOVEL INHIBITOR SCAFFOLDS AGAINST THE METALLO-BETA-LACTAMASE VIM-2 BY SPR BASED FRAGMENT SCREENING