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(-) Description

Title :  RIBOSOMAL RNAS AND PROTEINS AS WELL AS FACTORS
 
Authors :  K. Nagano, N. Nagano
Date :  17 May 01  (Deposition) - 24 Sep 03  (Release) - 24 Sep 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D,E
Keywords :  Translocation, Large Ribosomal Rna, Small Ribosomal Rna, Trna, Mrna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nagano, N. Nagano
Stereochemical Mechanism Of Translocation, Termination And Codon Recognition Of E. Coli 16S And 23S Ribosomal Rnas
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 16S RIBOSOMAL RNA
    Chains: A
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
 
Molecule 2 - 5'- R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U P*UP*UP*UP*U)-3'
    Chains: B
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
    Other Details: MESSENGER RNA
 
Molecule 3 - TRNAS BOUND TO A AND P SITES
    Chains: C, D
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
 
Molecule 4 - 23S RIBOSOMAL RNA
    Chains: E
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 29)

Theoretical Model (11, 29)
No.NameCountTypeFull Name
11MA2Mod. Nucleotide6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
22MG2Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
35MC4Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
45MU2Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
5H2U4Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
6M2G2Mod. NucleotideN2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
7OMC3Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
8OMG3Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
9OMU1Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
10PSU4Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
11YG2Mod. ResidueWYBUTOSINE

(-) Sites  (0, 0)

(no "Site" information available for 1IPL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IPL)

(-) Exons   (0, 0)

(no "Exon" information available for 1IPL)

(-) Sequences/Alignments

Theoretical Model
   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:RNA  Length:96
                                                                                                                                 
                1ipl A 1044 ACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAGAUGACGUCAAGUCAUCAUGgCCCUUACG 1215
                                  1053      1063      1073      1083      1093      1103      1189      1199      1209      
                                                                                           1110|                1207-OMG    
                                                                                            1187                            


Chain B from PDB  Type:RNA  Length:23
                                                        
                1ipl B 1623 UUUUUUUUUUUUUUUUUUUUUUU 1645
                                  1632      1642   


Chain C from PDB  Type:RNA  Length:92
                                                                                                                             
                1ipl C 1801 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAAUGCGGUCAAAAGCUGCAUCcUGUGuuCGaUCCACAGAAUUCGCACCA 1892
                                  1810     |1820     |1830 | |  1840      1850      1860    | 1870|  |  1880      1890  
                                  1810-2MG ||     1826-M2G | |  | ||                     1865-5MC||  |                  
                                        1816-H2U        1832-OMC| ||                          1870-5MU                  
                                         1817-H2U         1834-OMG||                           1871-PSU                 
                                                             1837-YG                              1874-1MA              
                                                               1839-PSU                                                 
                                                                1840-5MC                                                


Chain D from PDB  Type:RNA  Length:92
                                                                                                                             
                1ipl D 1901 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAAUGCGGUCAAAAGCUGCAUCcUGUGuuCGaUCCACAGAAUUCGCACCA 1992
                                  1910     |1920     |1930 | |  1940      1950      1960    | 1970|  |  1980      1990  
                                  1910-2MG ||     1926-M2G | |  | ||                     1965-5MC||  |                  
                                        1916-H2U        1932-OMC| ||                          1970-5MU                  
                                         1917-H2U         1934-OMG||                           1971-PSU                 
                                                             1937-YG                              1974-1MA              
                                                               1939-PSU                                                 
                                                                1940-5MC                                                


Chain E from PDB  Type:RNA  Length:634
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
                1ipl E 2406 GGGGGGACCAUCCUCCCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCAcCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCuGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCC 4788
                                  2415     |4026      4036      4046      4056      4066      4076      4234      4244      4254      4264      4274      4284      4294      4304      4314      4324      4334      4344      4354      4364      4374      4384      4394      4404      4414      4424      4434      4444      4454      4464      4474      4484      4494   |  4504      4514      4524      4534      4544      4554      4564      4574      4584      4594      4604      4614      4624      4634      4644      4654      4664      4674      4684      4694      4704      4714      4724      4734      4744      4754      4764      4774      4784    
                                        2421|                                                          4085|                                                                                                                                                                                                                                                                    4498-OMC                                              4552-OMU                                                                                                                                                                                                                                        
                                         4023                                                           4234
   Legend:   → Mismatch (orange background)
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  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 1IPL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IPL)

(-) Gene Ontology  (0, 0)

Theoretical Model(hide GO term definitions)
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1ip8 MODEL 1
1ipm MODEL 3
1ipn MODEL 4
1ipo MODEL 5
1ipq MODEL 6
1ipr MODEL 7
1ipu MODEL 8
1ipv MODEL 9
1ipx MODEL 10
1ipy MODEL 11
1ipz MODEL 12