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 :  CRYSTAL STRUCTURE OF RESPONSE REGULATOR RECEIVER DOMAIN PROTEIN (CHEY-LIKE) FROM METHANOSPIRILLUM HUNGATEI JF-1
 
Authors :  Y. Patskovsky, J. Freeman, S. Hu, K. Bain, D. Smith, S. R. Wasserman, J. M S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  04 Mar 08  (Deposition) - 11 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Unknown Function, Uncharacterized Protein, Signal Regulator Receiver Domain, Protein Structure Initiative, Psi- 2, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, J. Freeman, S. Hu, K. Bain, D. Smith, S. R. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Response Regulator Receiver Domain Protein (Chey-Like) From Methanospirillum Hungatei Jf-1.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RESPONSE REGULATOR RECEIVER DOMAIN PROTEIN (CHEY-LIKE)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: REC, MHUN_0886
    Organism Scientific: METHANOSPIRILLUM HUNGATEI JF-1
    Organism Taxid: 323259
    Strain: JF-1 / DSM 864

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
3MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:13 , ASP A:56 , HOH A:218 , HOH A:230 , HOH A:246BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREARG A:69 , LEU A:72 , ASP A:73 , PRO A:109 , HOH A:264BINDING SITE FOR RESIDUE GOL A 202
3AC3SOFTWAREGLN A:99 , HOH A:225 , HOH A:266 , HOH A:297 , HOH A:307BINDING SITE FOR RESIDUE GOL A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CG4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:108 -Pro A:109

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CG4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CG4)

(-) Exons   (0, 0)

(no "Exon" information available for 3CG4)

(-) 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:126
 aligned with Q2FQ04_METHJ | Q2FQ04 from UniProtKB/TrEMBL  Length:137

    Alignment length:126
                                    13        23        33        43        53        63        73        83        93       103       113       123      
         Q2FQ04_METHJ     4 HKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGFVRNQ 129
               SCOP domains d3cg4a_ A: automated matches                                                                                                   SCOP domains
               CATH domains 3cg4A00 A:4-129  [code=3.40.50.2300, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...eeeeee......hhhhhhhhhhhh.....eeeeeee..........hhhh.eeeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cg4 A   4 HKGDVmIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDImmPGmDGWDTIRAILDNSLEQGIAIVmLTAKNAPDAKmIGLQEYVVDYITKPFDNEDLIEKTTFFmGFVRNQ 129
                                 |  13        23        33        43        53    ||  63        73        83|       93 |     103       113       123      
                                 9-MSE                                           58-MSE                    84-MSE     95-MSE                     123-MSE  
                                                                                  59-MSE                                                                  
                                                                                     62-MSE
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CG4)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q2FQ04_METHJ | Q2FQ04)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:108 - Pro A:109   [ RasMol ]  
 

(-) 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
  3cg4
    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
  Q2FQ04_METHJ | Q2FQ04
    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
  Q2FQ04_METHJ | Q2FQ04
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3CG4)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3CG4)