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(-) Description

Title :  CATALYTIC RNA ENZYME-PRODUCT COMPLEX
 
Authors :  J. B. Murray, H. Szoke, A. Szoke, W. G. Scott
Date :  25 Feb 00  (Deposition) - 06 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Catalytic Rna, Ribozyme, Enzyme-Product Complex, Crystal Lattice Trapping (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Murray, H. Szoke, A. Szoke, W. G. Scott
Capture And Visualization Of A Catalytic Rna Enzyme-Product Complex Using Crystal Lattice Trapping And X-Ray Holographic Reconstruction.
Mol. Cell V. 5 279 2000
PubMed-ID: 10882069  |  Reference-DOI: 10.1016/S1097-2765(00)80423-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA RIBOZYME STRAND
    Chains: A
    Engineered: YES
    Other Details: 16-MER
    Synthetic: YES
 
Molecule 2 - FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE
    Chains: B
    Engineered: YES
    Other Details: 20-MER, 3'-END CYCLIC PHOSPHATE
    Synthetic: YES
 
Molecule 3 - SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE
    Chains: C
    Engineered: YES
    Other Details: 5-MER
    Synthetic: YES
 
Molecule 4 - UNCLEAVED RNA SUBSTRATE
    Chains: D
    Engineered: YES
    Other Details: 25-MER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2CD8Ligand/IonCADMIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG A:23BINDING SITE FOR RESIDUE CD A 1
2AC2SOFTWAREG A:50BINDING SITE FOR RESIDUE CD A 2
3AC3SOFTWAREG B:164 , G D:164BINDING SITE FOR RESIDUE CD B 3
4AC4SOFTWAREG B:114 , G D:114BINDING SITE FOR RESIDUE CD B 4
5AC5SOFTWAREG B:120 , G D:120BINDING SITE FOR RESIDUE CD B 5
6AC6SOFTWAREG A:25BINDING SITE FOR RESIDUE CD A 6
7AC7SOFTWAREG B:162 , G D:162BINDING SITE FOR RESIDUE CD B 7
8AC8SOFTWAREA A:90 , G A:101BINDING SITE FOR RESIDUE CD A 8

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 488D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 488D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 488D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 488D)

(-) Exons   (0, 0)

(no "Exon" information available for 488D)

(-) 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:RNA  Length:16
                                                
                 488d A  25 GUGGUCUGAUGAGGCC 104
                            ||||||||70|||   
                            |||||||60||||   
                           25|||||||70|||   
                            24|||||| 80||   
                             23|||||  90|   
                              22||||  101   
                               21|||        
                                30||        
                                 40|        
                                  50        


Chain B from PDB  Type:RNA  Length:20
                                                    
                 488d B 114 GGCCGAAACUCGUAAGAGUc 170
                            |||||||153|||||||170
                          114||||||| 31L||||||||
                           113||||||  32L|||||||
                            112|||||  |33L||||||
                             111||||  | 34L|||||
                              120|||  |  164||||
                               130||  |   163|||
                                140|  |    162||
                                 151  |     161|
                                    154      170-CCC


Chain C from PDB  Type:RNA  Length:5
                                     
                 488d C  11 ACCAC  15


Chain D from PDB  Type:RNA  Length:25
                                                         
                 488d D 114 GGCCGAAACUCGUAAGAGUCACCAC  15
                            |||||||153|||||||170|    
                          114||||||| 31L|||||||11    
                           113||||||  32L|||||||     
                            112|||||  |33L||||||     
                             111||||  | 34L|||||     
                              120|||  |  164||||     
                               130||  |   163|||     
                                140|  |    162||     
                                 151  |     161|     
                                    154      170
   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 488D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 488D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 488D)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 488D)

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  Cis Peptide Bonds
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  488d
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 Related Entries

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

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