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

(-) Description

Title :  APO GIM-1 WITH 2MOL. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO-BETA-LACTAMASES
 
Authors :  P. S. Borra, O. Samuelsen, J. Spencer, M. S. Lorentzen, H. -K. S. Leiros
Date :  18 Oct 12  (Deposition) - 24 Jul 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Antibiotic Resistance, Residue Determinants, Loop Dynamics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Borra, O. Samuelsen, J. Spencer, T. R. Walsh, M. S. Lorentzen, H. -K. S. Leiros
Crystal Structures Of Pseudomonas Aeruginosa Gim-1: Active- Site Plasticity In Metallo-Beta-Lactamases.
Antimicrob. Agents Chemother. V. 57 848 2013
PubMed-ID: 23208706  |  Reference-DOI: 10.1128/AAC.02227-12

(-) Compounds

Molecule 1 - GIM-1 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR PLYSS PRARE
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: METALLO-BETA-LACTAMASE GIM-1

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YNU)

(-) Sites  (0, 0)

(no "Site" information available for 2YNU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YNU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YNU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YNU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YNU)

(-) Exons   (0, 0)

(no "Exon" information available for 2YNU)

(-) 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:217
 aligned with Q704V1_PSEAI | Q704V1 from UniProtKB/TrEMBL  Length:250

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q704V1_PSEAI    22 KPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASN 238
               SCOP domains d2ynua_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeeehhhhhhhhhh......eee...eeee....eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ynu A  40 KPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASN 295
                                 || 50        60        70        80        90       100||  || 113       123       134       144     ||168      |181       191       201   || |217       227       237       247       257       278       288       
                                45|                                                  100||  ||                   131|              150|       175|                       205| ||                                               265|                  
                                 47                                                   102|  ||                    133               165        179                        209 ||                                                277                  
                                                                                       104  ||                                                                              211|                                                                     
                                                                                          107|                                                                               215                                                                     
                                                                                           109                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with Q704V1_PSEAI | Q704V1 from UniProtKB/TrEMBL  Length:250

    Alignment length:215
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
         Q704V1_PSEAI    22 KPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESA 236
               SCOP domains d2ynub_ B: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeee....eeee...........eeee....eeeeehhh........------hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ynu B  40 KPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGL------SISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESA 293
                                 || 50        60        70        80        90       100||  || 113       123       134       144     ||168      |181       191       201   || |217       227   |     -|      247       257       278       288     
                                45|                                                  100||  ||                   131|              150|       175|                       205| ||             231    238                        265|                
                                 47                                                   102|  ||                    133               165        179                        209 ||                                                277                
                                                                                       104  ||                                                                              211|                                                                   
                                                                                          107|                                                                               215                                                                   
                                                                                           109
   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  (0, 0)

(no "CATH Domain" information available for 2YNU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YNU)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q704V1_PSEAI | Q704V1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
(no "Ligands, Modified Residues, Ions" information available for 2ynu)
 
  Sites
(no "Sites" information available for 2ynu)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ynu)
 
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 | Biol. Unit 1 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
  2ynu
    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
  Q704V1_PSEAI | Q704V1
    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
  Q704V1_PSEAI | Q704V1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q704V1_PSEAI | Q704V1: 2ynt 2ynv 2ynw 5acp 5acq 5acr 5acs 5act

(-) Related Entries Specified in the PDB File

2ynt GIM-1-3MOL NATIVE. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO- BETA-LACTAMASES
2ynv CYS221 OXIDIZED, MONO ZINC GIM-1 - GIM-1-OX. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO-BETA-LACTAMASES
2ynw GIM-1-2MOL NATIVE. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO- BETA-LACTAMASES