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 :  ZN-BOUND FORM OF CUPRIAVIDUS METALLIDURANS CH34 CNRXS
 
Authors :  J. Trepreau, E. Girard, A. P. Maillard, E. De Rosny, I. Petit-Haertlei J. Coves
Date :  20 Dec 10  (Deposition) - 30 Mar 11  (Release) - 27 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Trepreau, E. Girard, A. P. Maillard, E. De Rosny, I. Petit-Haertlein, R. Kahn, J. Coves
Structural Basis For Metal Sensing By Cnrx.
J. Mol. Biol. V. 408 766 2011
PubMed-ID: 21414325  |  Reference-DOI: 10.1016/J.JMB.2011.03.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICKEL AND COBALT RESISTANCE PROTEIN CNRR
    Atcc: 43123
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET30
    Expression System Vector Type: PLASMID
    Fragment: METAL-SENSOR DOMAIN, RESIDUES 31-148
    Organism Scientific: CUPRIAVIDUS METALLIDURANS
    Organism Taxid: 266264
    Strain: CH34
    Synonym: NICKEL AND COBALT RESISTANCE PROTEIN CNRX

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2ZN3Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:38 , GLU A:63 , HIS A:119 , CL A:1146BINDING SITE FOR RESIDUE ZN A 149
2AC2SOFTWAREHIS A:42 , HIS A:46 , GLU A:60 , CL A:1147BINDING SITE FOR RESIDUE ZN A 150
3AC3SOFTWAREHIS B:42 , HIS B:46 , GLU B:63 , HIS B:119BINDING SITE FOR RESIDUE ZN B 149
4AC4SOFTWAREHIS A:38 , HIS A:42 , LEU A:45 , GLU A:63 , HIS A:119 , MET A:123 , ZN A:149BINDING SITE FOR RESIDUE CL A1146
5AC5SOFTWAREHIS A:42 , HIS A:46 , GLU A:60 , ZN A:150 , HOH B:2005 , HOH B:2007BINDING SITE FOR RESIDUE CL A1147
6AC6SOFTWAREALA A:67 , ARG A:70 , ARG A:71 , HOH A:2019BINDING SITE FOR RESIDUE CL A1148
7AC7SOFTWARETRP A:94 , PHE B:121BINDING SITE FOR RESIDUE CL A1149
8AC8SOFTWAREASP B:52 , ALA B:53BINDING SITE FOR RESIDUE CL B1149

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y3D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y3D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y3D)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y3D)

(-) 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:111
 aligned with CNRR_CUPMC | P37975 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:111
                                    44        54        64        74        84        94       104       114       124       134       144 
           CNRR_CUPMC    35 EAGHGDLHEILHEAVPLDANEREILELKEDAFAQRRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFEMRAGLKPEHRPAYDRVLIDALRR 145
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2y3d A  35 EAGHGDLHEILHEAVPLDANEREILELKEDAFAQRRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFEMRAGLKPEHRPAYDRVLIDALRR 145
                                    44        54        64        74        84        94       104       114       124       134       144 


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with CNRR_CUPMC | P37975 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:110
                                    48        58        68        78        88        98       108       118       128       138       148
           CNRR_CUPMC    39 GDLHEILHEAVPLDANEREILELKEDAFAQRRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFEMRAGLKPEHRPAYDRVLIDALRRGSQ 148
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2y3d B  39 GDLHEILHEAVPLDANEREILELKEDAFAQRRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFEMRAGLKPEHRPAYDRVLIDALRRGSQ 148
                                    48        58        68        78        88        98       108       118       128       138       148
   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 2Y3D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y3D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y3D)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CNRR_CUPMC | P37975)
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
    CL  [ 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 2y3d)
 

(-) 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
  2y3d
    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
  CNRR_CUPMC | P37975
    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)
  (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
  CNRR_CUPMC | P37975
    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
        CNRR_CUPMC | P37975: 2y39 2y3b 2y3g 2y3h 3epv 3zg1 4wwb 4wwd 4wwf

(-) Related Entries Specified in the PDB File

2y39 NI-BOUND FORM OF CUPRIAVIDUS METALLIDURANS CH34 CNRXS
2y3b CO-BOUND FORM OF CUPRIAVIDUS METALLIDURANS CH34 CNRXS
2y3g SE-MET FORM OF CUPRIAVIDUS METALLIDURANS CH34 CNRXS
2y3h E63Q MUTANT OF CUPRIAVIDUS METALLIDURANS CH34 CNRXS