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(-) Description

Title :  CROSSLINKED HAMMERHEAD RIBOZYME INITIAL STATE
 
Authors :  C. M. Dunham, J. B. Murray, W. G. Scott
Date :  12 Feb 03  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hammerhead Ribozyme Crosslink Conformational Change, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. M. Dunham, J. B. Murray, W. G. Scott
A Helical Twist-Induced Conformational Switch Activates Cleavage In The Hammerhead Ribozyme.
J. Mol. Biol. V. 332 327 2003
PubMed-ID: 12948485  |  Reference-DOI: 10.1016/S0022-2836(03)00843-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- R(P*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'
    ChainsA
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'- R(*GP*CP*CP*GP*AP*AP*AP*CP*UP*CP*GP*UP*AP*AP*GP*AP*GP*UP*CP *AP*CP*CP*AP*C)-3'
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CO4Ligand/IonCOBALT (II) ION
2G1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC B:122BINDING SITE FOR RESIDUE CO B 1
2AC2SOFTWAREG A:18BINDING SITE FOR RESIDUE CO A 2
3AC3SOFTWAREG A:14 , U A:15BINDING SITE FOR RESIDUE CO B 3
4AC4SOFTWAREU A:20 , U B:119BINDING SITE FOR RESIDUE CO B 4
5AC5SOFTWAREG A:11 , C A:26 , G B:102BINDING SITE FOR RESIDUE G A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NYI)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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Chain A from PDB  Type:RNA  Length:17
                                                 
                 1nyi A  11 GUGGUCUGAUGAGGCCG 500
                                    20     ||
                                          26|
                                          500

Chain B from PDB  Type:RNA  Length:24
                                                        
                 1nyi B 102 GCCGAAACUCGUAAGAGUCACCAC 125
                                   111       121    

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  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 1NYI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1NYI)

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