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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS PYROPHOSPHOHYDROLASE BSRPPH BOUND TO A NON-HYDROLYSABLE TRIPHOSPHORYLATED DINUCLEOTIDE RNA (PCP-PGPG) - FIRST GUANOSINE RESIDUE IN GUANOSINE BINDING POCKET
 
Authors :  J. Piton, V. Larue, Y. Thillier, A. Dorleans, O. Pellegrini, I. Li De L Gallay, J. J. Vasseur, F. Debart, C. Tisne, C. Condon
Date :  03 Apr 13  (Deposition) - 08 May 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nudix Hydrolase, Rna Pyrophosphohydrolase, Rpph, Cytosol, Hydrolase, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Piton, V. Larue, Y. Thillier, A. Dorleans, O. Pellegrini, I. Li De La Sierra-Gallay, J. J. Vasseur, F. Debart, C. Tisne, C. Condon
Bacillus Subtilis Rna Deprotection Enzyme Rpph Recognizes Guanosine In The Second Position Of Its Substrates.
Proc. Natl. Acad. Sci. Usa V. 110 8858 2013
PubMed-ID: 23610407  |  Reference-DOI: 10.1073/PNAS.1221510110

(-) Compounds

Molecule 1 - RNA PYROPHOSPHOHYDROLASE
    Chains: A, B
    EC Number: 3.6.1.55
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: BSU30630, MUTTA, YTKD
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: 8-OXO-DGTPASE, 7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE, DGTP PYROPHOSPHOHYDROLASE
 
Molecule 2 - RNA (5'-R(*(GCP)P*G)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (1x):  B 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GCP1Mod. NucleotidePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GCP1Mod. NucleotidePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GCP-1Mod. NucleotidePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:48 , VAL A:120 , LEU A:121 , PHE A:122 , HIS A:123 , GLU A:124 , GLU B:42 , TYR B:48 , LEU B:121 , PHE B:122 , HIS B:123 , HOH B:319 , HOH B:321 , HOH B:398 , HOH B:404BINDING SITE FOR RESIDUE EPE B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JZU)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee...........eeeeeeee..eeeeeee...eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeee....eeeeeeeeeeeeee........eeeeeee.....hhhhh...hhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzu A   1 MYEFKDYYQNTVQLSFDDQPFSDSPKHVWVICRFGGKWLLTEHEDRGYEFPGGKVEPMECAEEAALREVKEETGARVKSLKYLGQYKVLGKEKVIVKNIYFADIEKLEKQADYFETKGPVLFHELPENLSRNKKFSFIMKDSVLPISLKKLKESGWI 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee...........eeeeeeee..eeeeeee...eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeee.eeeeeeeeeeee........eeeeeee.....hhhhh...hhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzu B   1 MYEFKDYYQNTVQLSFDDQPFSDSPKHVWVICRFGGKWLLTEHEDRGYEFPGGKVEPMECAEEAALREVKEETGARVKSLKYLGQYKVLIVKNIYFADIEKLEKQADYFETKGPVLFHELPENLSRNKKFSFIMKDSVLPISLKKLKESGW 156
                                    10        20        30        40        50        60        70        80        95       105       115       125       135       145       155 
                                                                                                                   89|                                                             
                                                                                                                    95                                                             


Chain C from PDB  Type:DNA/RNA  Length:2
                                  
                 4jzu C   1 xG   2
                            | 
                            1-GCP
   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 4JZU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JZU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GCP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jzu)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  4jzu
    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
  YTKD_BACSU | O35013
    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)
  3.6.1.55
    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
  YTKD_BACSU | O35013
    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
        YTKD_BACSU | O35013: 4jzs 4jzt 4jzv

(-) Related Entries Specified in the PDB File

4jzs 4jzt 4jzv