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

(-) Description

Title :  NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 4 INTERMEDIARY SITES
 
Authors :  C. Dian, K. Schauer, U. Kapp, S. M. Mcsweeney, A. Labigne, L. Terradot
Date :  21 Dec 05  (Deposition) - 17 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Nickel Uptake, Transcription Regulator, Ribbon-Helix-Helix, Acidic-Adaptive Response, Transcriptional Regulation, Dna- Binding, Hypothetical Protein, Metal-Binding, Nickel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dian, K. Schauer, U. Kapp, S. M. Mcsweeney, A. Labigne, L. Terradot
Structural Basis Of The Nickel Response In Helicobacter Pylori: Crystal Structures Of Hpnikr In Apo And Nickel-Bound States.
J. Mol. Biol. V. 361 715 2006
PubMed-ID: 16872629  |  Reference-DOI: 10.1016/J.JMB.2006.06.058

(-) Compounds

Molecule 1 - PUTATIVE NICKEL-RESPONSIVE REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL12Ligand/IonGLYCEROL
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:101 , GLN B:87 , HIS B:93 , NI B:1151BINDING SITE FOR RESIDUE CL B1150
2AC2SOFTWAREHIS A:74 , HIS B:88 , CL B:1150BINDING SITE FOR RESIDUE NI B1151
3AC3SOFTWAREHIS A:88 , HIS B:74 , HIS B:75 , HIS B:101BINDING SITE FOR RESIDUE NI B1152
4AC4SOFTWAREGLU A:78 , GLN A:81 , ARG A:82 , HOH A:2016 , HOH A:2028 , ARG B:77 , GLU B:78BINDING SITE FOR RESIDUE GOL A1142
5AC5SOFTWARELEU A:130 , ARG A:131 , GLY A:132 , VAL A:133 , HOH A:2029 , HOH A:2030BINDING SITE FOR RESIDUE GOL A1143
6AC6SOFTWAREASN A:80 , MET A:83 , GLN A:87 , THR A:97 , GLU A:109 , ILE A:111 , HOH A:2031BINDING SITE FOR RESIDUE GOL A1144
7AC7SOFTWAREVAL A:94 , LEU A:95 , ILE B:100 , HIS B:101BINDING SITE FOR RESIDUE GOL A1145
8AC8SOFTWAREASN B:80 , MET B:83 , GLU B:109 , HOH B:2033BINDING SITE FOR RESIDUE GOL B1148
9AC9SOFTWAREGLN A:81 , ASP A:85 , HIS A:88 , HIS B:74 , HIS B:75 , ARG B:77BINDING SITE FOR RESIDUE GOL B1149

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CAJ)

(-) 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:128
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:133
                                    18        28        38        48        58        68        78        88        98       108       118       128       138   
           NIKR_HELPY     9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
               SCOP domains d2caja1 A:9-60 automated matches                    d2caja2 A:61-141 automated matches                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhhh.....hhhhhhhhhhhh....-----......eeeeeeeeee.....hhhhhhhhhhhhh.eeeeeeeee....eeeeeeeeee.hhhhhhhhhhhh....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2caj A   9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVED-----NPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKA 141
                                    18        28        38        48   |    58        68        78        88        98       108       118       128       138   
                                                                      52    58                                                                                   


Chain B from PDB  Type:PROTEIN  Length:139
 aligned with NIKR_HELPY | O25896 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:139
                                    18        28        38        48        58        68        78        88        98       108       118       128       138         
           NIKR_HELPY     9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYN 147
               SCOP domains d2cajb1 B:9-60 automated matches                    d2cajb2 B:61-147 automated matches                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........eeeeeeeeee....hhhhhhhhhhhhh..eeeeeeeee....eeeeeeeeee.hhhhhhhhhhhh....eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2caj B   9 SIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYN 147
                                    18        28        38        48        58        68        78        88        98       108       118       128       138
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NIKR_HELPY | O25896)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010045    response to nickel cation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nickel cation stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2caj)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  2caj
    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
  NIKR_HELPY | O25896
    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
  NIKR_HELPY | O25896
    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
        NIKR_HELPY | O25896: 2ca9 2cad 2wvb 2wvc 2wvd 2wve 2wvf 3lgh 3pht 3qsi

(-) Related Entries Specified in the PDB File

2ca9 APO-HPNIKR IN CLOSED TRANS-CONFORMATION
2cad NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 2F, 2X AND 2I SITES