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

(-) Description

Title :  CRYSTAL STRUCTURE OF NDX2 FROM THERMUS THERMOPHILUS HB8
 
Authors :  T. Wakamatsu, N. Nakagawa, S. Kuramitsu, S. Yokoyama, R. Masui, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Apr 07  (Deposition) - 26 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nudix Protein, Adp-Ribose, Fad, Thermus Thermophilus, Hydrolas, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wakamatsu, N. Nakagawa, S. Kuramitsu, R. Masui
Structural Basis For Different Substrate Specificities Of Two Adp-Ribose Pyrophosphatases From Thermus Thermophilus Hb8
J. Bacteriol. V. 190 1108 2008
PubMed-ID: 18039767  |  Reference-DOI: 10.1128/JB.01522-07

(-) Compounds

Molecule 1 - MUTT/NUDIX FAMILY PROTEIN
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NDX2
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: NDX2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YVN)

(-) Sites  (0, 0)

(no "Site" information available for 2YVN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:15 -Pro A:16
2Gly A:39 -Pro A:40

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVN)

(-) 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:182
 aligned with Q5SJY9_THET8 | Q5SJY9 from UniProtKB/TrEMBL  Length:182

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
         Q5SJY9_THET8     1 MSPWERILLEEILSEPVRLVKERVRTHTGRELTYVYRPGPVAASFVLPVTERGTALLVRQYRHPTGKFLLEVPAGKVDEGETPEAAARRELREEVGAEAETLIPLPSFHPQPSFTAVVFHPFLALKARVVTPPTLEEGELLESLELPLTEVYALLAKGEIQDASTALTLFYAEPHLKRLGLL 182
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------NUDIX-2yvnA01 A:40-171                                                                                                              ----------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....eeeeeee.....eeeeee.....eeeeeee.....eeeeeeeeehhhheeeee..eee.....hhhhhhhhhhhhhhhee...eee.............eeeeeee...ee...........eeeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvn A   1 MSPWERILLEEILSEPVRLVKERVRTHTGRELTYVYRPGPVAASFVLPVTERGTALLVRQYRHPTGKFLLEVPAGKVDEGETPEAAARRELREEVGAEAETLIPLPSFHPQPSFTAVVFHPFLALKARVVTPPTLEEGELLESLELPLTEVYALLAKGEIQDASTALTLFYAEPHLKRLGLL 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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 2YVN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5SJY9_THET8 | Q5SJY9)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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
(no "Ligands, Modified Residues, Ions" information available for 2yvn)
 
  Sites
(no "Sites" information available for 2yvn)
 
  Cis Peptide Bonds
    Glu A:15 - Pro A:16   [ RasMol ]  
    Gly A:39 - Pro A:40   [ RasMol ]  
 
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 | Biol. Unit 1 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
  2yvn
    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
  Q5SJY9_THET8 | Q5SJY9
    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)
  3.6.1.-
    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
  Q5SJY9_THET8 | Q5SJY9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5SJY9_THET8 | Q5SJY9: 2yvm 2yvo 2yvp

(-) Related Entries Specified in the PDB File

2yvm
2yvo
2yvp RELATED ID: TTK003001256.3 RELATED DB: TARGETDB