Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHOROLYTIC EXORIBONUCLEASE RNASE PH FROM BACILLUS SUBTILIS
 
Authors :  L. S. Harlow, A. Kadziola, K. F. Jensen, S. Larsen
Date :  07 Apr 03  (Deposition) - 09 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Transferase, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. S. Harlow, A. Kadziola, K. F. Jensen, S. Larsen
Crystal Structure Of The Phosphorolytic Exoribonuclease Rnase Ph From Bacillus Subtilis And Implications For Its Quaternary Structure And Trna Binding.
Protein Sci. V. 13 668 2004
PubMed-ID: 14767080  |  Reference-DOI: 10.1110/PS.03477004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE PH
    Chains: A, B, C, D, E, F
    EC Number: 2.7.7.56
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: RNASE PH, TRNA NUCLEOTIDYLTRANSFERASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:86 , GLY A:124 , THR A:125 , ARG A:126BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWARETRP A:58 , THR A:60 , ARG A:99BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREARG B:86 , GLY B:124 , THR B:125 , ARG B:126BINDING SITE FOR RESIDUE SO4 B 303
04AC4SOFTWARETRP B:58 , THR B:60 , ARG B:99BINDING SITE FOR RESIDUE SO4 B 304
05AC5SOFTWAREARG C:86 , GLY C:124 , THR C:125 , ARG C:126BINDING SITE FOR RESIDUE SO4 C 305
06AC6SOFTWARETRP C:58 , THR C:60 , ARG C:99BINDING SITE FOR RESIDUE SO4 C 306
07AC7SOFTWAREARG D:86 , GLY D:124 , THR D:125 , ARG D:126BINDING SITE FOR RESIDUE SO4 D 307
08AC8SOFTWARETRP D:58 , THR D:60 , ARG D:99BINDING SITE FOR RESIDUE SO4 D 308
09AC9SOFTWAREARG E:86 , GLY E:124 , THR E:125 , ARG E:126BINDING SITE FOR RESIDUE SO4 E 309
10BC1SOFTWARETRP E:58 , THR E:60 , ARG E:99BINDING SITE FOR RESIDUE SO4 E 310
11BC2SOFTWAREARG F:86 , GLY F:124 , THR F:125 , ARG F:126BINDING SITE FOR RESIDUE SO4 F 311
12BC3SOFTWARETRP F:58 , THR F:60 , ARG F:99BINDING SITE FOR RESIDUE SO4 F 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OYP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OYP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OYP)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PHPS01277 Ribonuclease PH signature.RNPH_BACSU116-128
 
 
 
 
 		  6A:116-128
B:116-128
C:116-128
D:116-128
E:116-128
F:116-128

(-) Exons   (0, 0)

(no "Exon" information available for 1OYP)

(-) 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:226
 aligned with RNPH_BACSU | P28619 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           RNPH_BACSU     1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
               SCOP domains d1oypa1 A:1-151 Ribonuclease PH, domain 1                                                                                                              d1oypa2 A:152-243 Ribonuclease PH, domain 2                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.......eeeeeee..eeeeeeeeee.............eeeeeee..-----------------hhhhhhhhhhhhhhhhh..hhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee...eeee..hhhhhhhh.eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyp A   1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSML-----------------SGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
                                    10        20        30        40        50        60     |   -         -   |    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                                                            66                84                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with RNPH_BACSU | P28619 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           RNPH_BACSU     1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
               SCOP domains d1oypb1 B:1-151 Ribonuclease PH, domain 1                                                                                                              d1oypb2 B:152-243 Ribonuclease PH, domain 2                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.......eeeeeee..eeeeeeeeee.............eeeeeee..-----------------hhhhhhhhhhhhhhhhh..hhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee...eeee..hhhhhhhh.eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyp B   1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSML-----------------SGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
                                    10        20        30        40        50        60     |   -         -   |    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                                                            66                84                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:226
 aligned with RNPH_BACSU | P28619 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           RNPH_BACSU     1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
               SCOP domains d1oypc1 C:1-151 Ribonuclease PH, domain 1                                                                                                              d1oypc2 C:152-243 Ribonuclease PH, domain 2                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.......eeeeeee..eeeeeeeeee.............eeeeeee..-----------------hhhhhhhhhhhhhhhhh..hhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee...eeee..hhhhhhhh.eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyp C   1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSML-----------------SGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
                                    10        20        30        40        50        60     |   -         -   |    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                                                            66                84                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:226
 aligned with RNPH_BACSU | P28619 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           RNPH_BACSU     1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
               SCOP domains d1oypd1 D:1-151 Ribonuclease PH, domain 1                                                                                                              d1oypd2 D:152-243 Ribonuclease PH, domain 2                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.......eeeeeee..eeeeeeeeee.............eeeeeee..-----------------hhhhhhhhhhhhhhhhh..hhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee...eeee..hhhhhhhh.eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyp D   1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSML-----------------SGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
                                    10        20        30        40        50        60     |   -         -   |    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                                                            66                84                                                                                                                                                               


Chain E from PDB  Type:PROTEIN  Length:226
 aligned with RNPH_BACSU | P28619 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           RNPH_BACSU     1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
               SCOP domains d1oype1 E:1-151 Ribonuclease PH, domain 1                                                                                                              d1oype2 E:152-243 Ribonuclease PH, domain 2                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.......eeeeeee..eeeeeeeeee.............eeeeeee..-----------------hhhhhhhhhhhhhhhhh..hhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee...eeee..hhhhhhhh.eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyp E   1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSML-----------------SGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
                                    10        20        30        40        50        60     |   -         -   |    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                                                            66                84                                                                                                                                                               


Chain F from PDB  Type:PROTEIN  Length:226
 aligned with RNPH_BACSU | P28619 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           RNPH_BACSU     1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
               SCOP domains d1oypf1 F:1-151 Ribonuclease PH, domain 1                                                                                                              d1oypf2 F:152-243 Ribonuclease PH, domain 2                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------RNase_PH-1oypF01 F:10-141                                                                                                           ---------------RNase_PH_C-1oypF07 F:157-225                                         ------------------ Pfam domains (1)
           Pfam domains (2) ---------RNase_PH-1oypF02 F:10-141                                                                                                           ---------------RNase_PH_C-1oypF08 F:157-225                                         ------------------ Pfam domains (2)
           Pfam domains (3) ---------RNase_PH-1oypF03 F:10-141                                                                                                           ---------------RNase_PH_C-1oypF09 F:157-225                                         ------------------ Pfam domains (3)
           Pfam domains (4) ---------RNase_PH-1oypF04 F:10-141                                                                                                           ---------------RNase_PH_C-1oypF10 F:157-225                                         ------------------ Pfam domains (4)
           Pfam domains (5) ---------RNase_PH-1oypF05 F:10-141                                                                                                           ---------------RNase_PH_C-1oypF11 F:157-225                                         ------------------ Pfam domains (5)
           Pfam domains (6) ---------RNase_PH-1oypF06 F:10-141                                                                                                           ---------------RNase_PH_C-1oypF12 F:157-225                                         ------------------ Pfam domains (6)
         Sec.struct. author .............eeeee.......eeeeeee..eeeeeeeeee.............eeeeeee..-----------------hhhhhhhhhhhhhhhhh..hhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee...eeee..hhhhhhhh.eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oyp F   1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSML-----------------SGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPE 243
                                    10        20        30        40        50        60     |   -         -   |    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                                                            66                84
   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, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OYP)

(-) Pfam Domains  (2, 12)

Asymmetric/Biological Unit
(-)
Clan: S5 (103)
(-)
Clan: no clan defined [family: RNase_PH_C] (9)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (RNPH_BACSU | P28619)
molecular function
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0009022    tRNA nucleotidyltransferase activity    Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate.
    GO:0004549    tRNA-specific ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in tRNA molecules.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0031125    rRNA 3'-end processing    Any process involved in forming the mature 3' end of an rRNA molecule.
    GO:0016075    rRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

 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
    SO4  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1oyp)
 

(-) 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
  1oyp
    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
  RNPH_BACSU | P28619
    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)
  2.7.7.56
    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
  RNPH_BACSU | P28619
    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
        RNPH_BACSU | P28619: 1oyr 1oys

(-) Related Entries Specified in the PDB File

1oyr CRYSTAL STRUCTURE OF THE PHOSPHOROLYTIC EXORIBONUCLEASE RNASE PH FROM BACILLUS SUBTILIS
1oys CRYSTAL STRUCTURE OF THE PHOSPHOROLYTIC EXORIBONUCLEASE RNASE PH FROM BACILLUS SUBTILIS