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 :  1.75 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A PUTATIVE NTP PYROPHOSPHOHYDROLASE (YFAO) FROM SALMONELLA TYPHIMURIUM LT2
 
Authors :  A. S. Halavaty, G. Minasov, L. Shuvalova, J. Winsor, I. Dubrovska, S. Pe W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  16 Aug 10  (Deposition) - 06 Oct 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. Lt2, Unknown Function, Putative Ntp Pyrophosphohydrolase, Infectious Diseases, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Csgid), Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, G. Minasov, L. Shuvalova, J. Winsor, I. Dubrovska, S. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 75 Angstrom Resolution Crystal Structure Of A Putative Nt Pyrophosphohydrolase (Yfao) From Salmonella Typhimurium Lt2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE TRIPHOSPHATASE NUDI
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMSCG7
    Expression System Strain: BL21(DE3)/MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NUDI, STM2295, YFAO
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1BME3Ligand/IonBETA-MERCAPTOETHANOL
2PO45Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:8 , TYR A:93 , ALA A:130 , THR A:134 , HOH A:251BINDING SITE FOR RESIDUE BME A 142
2AC2SOFTWAREGLN A:61 , GLU A:88 , ILE A:105 , CYS A:106 , ALA A:123 , HOH A:235BINDING SITE FOR RESIDUE BME A 143
3AC3SOFTWAREARG A:45BINDING SITE FOR RESIDUE PO4 A 144
4AC4SOFTWAREARG A:45 , GLU A:47 , GLU A:48 , ARG A:51 , HOH A:171 , HOH A:264BINDING SITE FOR RESIDUE PO4 A 145
5AC5SOFTWAREARG A:77 , ASN A:128 , HOH A:185 , HOH A:219 , HOH A:269 , HOH A:284 , PHE B:29BINDING SITE FOR RESIDUE PO4 A 146
6AC6SOFTWAREARG A:51 , ARG A:55 , HOH A:179 , HOH A:215BINDING SITE FOR RESIDUE PO4 A 147
7AC7SOFTWARECYS B:8 , TYR B:93 , ALA B:130 , THR B:134 , HOH B:201BINDING SITE FOR RESIDUE BME B 142
8AC8SOFTWAREARG B:4 , GLY B:38 , GLY B:39 , ARG B:52 , GLU B:53 , HOH B:163 , HOH B:219 , HOH B:242BINDING SITE FOR RESIDUE PO4 B 143

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OGA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUDI_SALTY1-141  1A:1-141
2NUDIX_BOXPS00893 Nudix box signature.NUDI_SALTY38-59
 		  2A:38-59
B:38-59

(-) Exons   (0, 0)

(no "Exon" information available for 3OGA)

(-) 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:134
 aligned with NUDI_SALTY | Q8ZNF5 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:142
                             1                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139  
           NUDI_SALTY     - -MRQRTIVCPLIQNDGCYLLCKMADNRGVFPGQWALSGGGVEPGERIEEALRREIREELGEQLILSDITPWTFRDDIRIKTYADGRQEEIYMIYLIFDCVSANRDICINDEFQDYAWVKPEELALYDLNVATRHTLALKGLL 141
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eeeeeee..------..ee...ee.....hhhhhhhhhhhhhhh....eeeeeeeeeeeeeeeee.--..eeeeeeeeeeeeeee..........eeeeeeehhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -NUDIX  PDB: A:1-141 UniProt: 1-141                                                                                                            PROSITE (1)
                PROSITE (2) --------------------------------------NUDIX_BOX  PDB: A:38-5---------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oga A   0 AMRQRTIVCPLIQNDGCYLLCKMAD------GQWALSGGGVEPGERIEEALRREIREELGEQLILSDITPWTFRDDIRIKTY--GRQEEIYMIYLIFDCVSANRDICINDEFQDYAWVKPEELALYDLNVATRHTLALKGLL 141
                                     9        19    |    - |      39        49        59        69        79 |  |   89        99       109       119       129       139  
                                                   24     31                                                81 84                                                         


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with NUDI_SALTY | Q8ZNF5 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
           NUDI_SALTY     2 RQRTIVCPLIQNDGCYLLCKMADNRGVFPGQWALSGGGVEPGERIEEALRREIREELGEQLILSDITPWTFRDDIRIKTYADGRQEEIYMIYLIFDCVSANRDICINDEFQDYAWVKPEELALYDLNVATRHTLALKGLL 141
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) NUDIX-3ogaB01 B:2-140                                                                                                                      - Pfam domains (1)
           Pfam domains (2) NUDIX-3ogaB02 B:2-140                                                                                                                      - Pfam domains (2)
         Sec.struct. author .eeeeeeeeeee..eeeeeee..........ee...ee.....hhhhhhhhhhhhhhh....eeeeeeeeeeee..-----------.eeeeeeeeeee..........eeeeeeehhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: - UniProt: 1-141                                                                                                                 PROSITE (1)
                PROSITE (2) ------------------------------------NUDIX_BOX  PDB: B:38-5---------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oga B   2 RQRTIVCPLIQNDGCYLLCKMADNRGVFPGQWALSGGGVEPGERIEEALRREIREELGEQLILSDITPWTFRDDIR-----------IYMIYLIFDCVSANRDICINDEFQDYAWVKPEELALYDLNVATRHTLALKGLL 141
                                    11        21        31        41        51        61        71     |   -       |91       101       111       121       131       141
                                                                                                      77          89
   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 3OGA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OGA)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NUDI_SALTY | Q8ZNF5)
molecular function
    GO:0047840    dCTP diphosphatase activity    Catalysis of the reaction: dCTP + H2O = dCMP + diphosphate.
    GO:0004170    dUTP diphosphatase activity    Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
    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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0047429    nucleoside-triphosphate diphosphatase activity    Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.

 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
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3oga)
 

(-) 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
  3oga
    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
  NUDI_SALTY | Q8ZNF5
    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)
  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
  NUDI_SALTY | Q8ZNF5
    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
        NUDI_SALTY | Q8ZNF5: 3n77

(-) Related Entries Specified in the PDB File

3n77 CRYSTAL STRUCTURE OF IDP01880, PUTATIVE NTP PYROPHOSPHOHYDROLASE OF SALMONELLA TYPHIMURIUM LT2 RELATED ID: IDP01880 RELATED DB: TARGETDB