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 :  CRYSTAL STRUCTURE OF S32A OF ST1022-GLN COMPLEX FROM SULFOLOBUS TOKODAII
 
Authors :  T. S. Kumarevel, P. Karthe, N. Nakano, A. Shinkai, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 Apr 07  (Deposition) - 29 Apr 08  (Release) - 17 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Transcriptional Regulator, Lrp/Asnc Family Gln Binding, St1022, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Kumarevel, N. Nakano, K. Ponnuraj, S. C. Gopinath, K. Sakamoto, A. Shinkai, P. K. Kumar, S. Yokoyama
Crystal Structure Of Glutamine Receptor Protein From Sulfolobus Tokodaii Strain 7 In Complex With Its Effector L-Glutamine: Implications Of Effector Binding In Molecular Association And Dna Binding
Nucleic Acids Res. V. 36 4808 2008
PubMed-ID: 18653535  |  Reference-DOI: 10.1093/NAR/GKN456
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 150AA LONG HYPOTHETICAL TRANSCRIPTIONAL REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ST1022
    Mutation: YES
    Organism Scientific: SULFOLOBUS TOKODAII
    Organism Taxid: 111955
    Synonym: ST1022

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GLN1Mod. Amino AcidGLUTAMINE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1GLN8Mod. Amino AcidGLUTAMINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:51 , ASN A:146BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWARETYR A:73 , TYR A:77 , PHE A:96 , LEU A:98 , GLY A:99 , ASN A:101 , ASP A:102 , LEU A:120 , MET A:124 , THR A:132 , SER A:133 , THR A:134 , HOH A:1007BINDING SITE FOR RESIDUE GLN A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PN6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PN6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PN6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PN6)

(-) Exons   (0, 0)

(no "Exon" information available for 2PN6)

(-) 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:151
 aligned with F9VNT4_SULTO | F9VNT4 from UniProtKB/TrEMBL  Length:150

    Alignment length:151
                                                                                                                                                                               150 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
        F9VNT4_SULTO      1 MDEIDLRILKILQYNAKYSLDEIAREIRIPKSTLSYRIKKLEKDGVIKGYYAYINPASLNLDYIVITSVKAKYGKNYHVELGNKLAQIPGVWGVYFVLGDNDFIVMARYKTREEFMEKFLERVMSIPEVERTSTQVVVKIIKESPNIVIF-    -
               SCOP domains d2pn6a1 A:1-60 automated matches                            d2pn6a2 A:61-150 automated matches                                                        - SCOP domains
               CATH domains 2pn6A01 A:1-52                                      2pn6A02 A:53-150  [code=3.30.70.920, no name defined]                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhh..........hhhhhh..eeeeeeeee....hhhhhhhhhhhh...eeeeee......eeeeeee.hhhhhhhhhhhhhh....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2pn6 A    1 MDEIDLRILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGYYAYINPASLNLDYIVITSVKAKYGKNYHVELGNKLAQIPGVWGVYFVLGDNDFIVMARYKTREEFMEKFLERVMSIPEVERTSTQVVVKIIKESPNIVIFQ 1002
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|
                                                                                                                                                                               150|
                                                                                                                                                                               1002
   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, 2)

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

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PN6)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (F9VNT4_SULTO | F9VNT4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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 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
    GLN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2pn6)
 
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
  2pn6
    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
  F9VNT4_SULTO | F9VNT4
    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
  F9VNT4_SULTO | F9VNT4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        F9VNT4_SULTO | F9VNT4: 2e7w 2e7x 2efn 2efo 2efp 2efq 2pmh 2yx4 2yx7

(-) Related Entries Specified in the PDB File

2e7w WILD TYPE
2e7x COMPLEXED WITH GLN
2efn S32A MUTANT
2efo Y77A MUTANT
2efp Y77A COMPLEXED WITH GLN
2efq T134A COMPLEXED WITH GLN RELATED ID: STO001001022.9 RELATED DB: TARGETDB
2pmh T132A MUTANT