Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 THE SINGLE-STRANDED RNA BINDING PROTEIN HUTP FROM GEOBACILLUS THERMODENITRIFICANS
 
Authors :  V. Thiruselvam, M. N. Ponnuswamy, T. S. Kumarevel
Date :  22 Jan 14  (Deposition) - 19 Mar 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Antitermination, Single Stranded-Rna Binding Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Thiruselvam, P. Sivaraman, T. Kumarevel, M. N. Ponnuswamy
Crystal Structure Of The Single-Stranded Rna Binding Protei Hutp From Geobacillus Thermodenitrificans
Biochem. Biophys. Res. Commun. V. 446 945 2014
PubMed-ID: 24650662  |  Reference-DOI: 10.1016/J.BBRC.2014.03.036

(-) Compounds

Molecule 1 - HUT OPERON POSITIVE REGULATORY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PHCE
    Gene: GTNG_0361, HUTP
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS NG80-2
    Organism Taxid: 420246
    Strain: NG80-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1HIS2Mod. Amino AcidHISTIDINE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1HIS6Mod. Amino AcidHISTIDINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:74 , HIS A:78 , HIS A:139 , HIS A:202 , HOH A:328BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWARETYR A:70 , HIS A:74 , TYR A:77 , HIS A:78 , ARG A:89 , ARG A:99 , ILE A:130 , GLY A:131 , ALA A:132 , HIS A:139 , MG A:201 , HOH A:329BINDING SITE FOR RESIDUE HIS A 202
3AC3SOFTWAREHIS B:74 , HIS B:78 , HIS B:139 , HIS B:202 , HOH B:328BINDING SITE FOR RESIDUE MG B 201
4AC4SOFTWARETYR B:70 , HIS B:74 , TYR B:77 , HIS B:78 , ARG B:89 , ARG B:99 , ILE B:130 , GLY B:131 , ALA B:132 , HIS B:139 , MG B:201 , HOH B:327BINDING SITE FOR RESIDUE HIS B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OKQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OKQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OKQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OKQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4OKQ)

(-) 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:146
                                                                                                                                                                                  
               SCOP domains d4okqa_ A: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee.........eeeeeeeeeeee......eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4okq A   4 EKSVRIGRQALLLAMLDEGEEGAILDELRASNWRYCQGRVGAMEPQKIVAAIETAAKRHEVVDGSLYRDMHALYHAILEAVHGVTRGQVELGDLLRTAGLRFAVVRGTPYEQPKEGEWIAVALYGTIGAPVRGLEHEAVGLGINHI 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      


Chain B from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains d4okqb_ B: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhh.eeeeeeeeeee....hhhhh.eeeeeeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4okq B   4 EKSVRIGRQALLLAMLDEGEEGAILDELRASNWRYCQGRVGAMEPQKIVAAIETAAKRHEVVDGSLYRDMHALYHAILEAVHGVTRGQVELGDLLRTAGLRFAVVRGTPYEQPKEGEWIAVALYGTIGAPVRGLEHEAVGLGINHI 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
   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 4OKQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OKQ)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

 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
    HIS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4okq)
 
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
  4okq
    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
  HUTP_GEOTN | A4IK89
    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
  HUTP_GEOTN | A4IK89
    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
        HUTP_GEOTN | A4IK89: 4ok9

(-) Related Entries Specified in the PDB File

4ok9 HUTP TERNARY COMPLEX FROM GEOBACILLUS THERMODENITRIFICANS