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(-) Description

Title :  AN ALL-RNA HAIRPIN RIBOZYME A38N1DA38 VARIANT WITH A TRANSITION-STATE MIMIC SUBSTRATE STRAND
 
Authors :  R. C. Spitale, R. Volpini, M. G. Heller, J. Krucinska, G. Cristalli, J. E. Wedekind
Date :  26 Mar 09  (Deposition) - 21 Apr 09  (Release) - 12 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hairpin Ribozyme, Rna Ribozyme, N1-Deazaadenosine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. Spitale, R. Volpini, M. G. Heller, J. Krucinska, G. Cristalli, J. E. Wedekind
Identification Of An Imino Group Indispensable For Cleavage By A Small Ribozyme.
J. Am. Chem. Soc. V. 131 6093 2009
PubMed-ID: 19354216  |  Reference-DOI: 10.1021/JA900450H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA (5'- R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3')
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)- 3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - RNA (5'- R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - RNA (5'- R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) -3')
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1NCO2Ligand/IonCOBALT HEXAMMINE(III)
2S9L1Ligand/Ion2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGENPHOSPHATE
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU A:1 , G B:13 , G C:15 , A C:31BINDING SITE FOR RESIDUE S9L B 14
2AC2SOFTWAREA C:20 , G C:21 , A D:40 , U D:41BINDING SITE FOR RESIDUE NCO C 1
3AC3SOFTWAREC A:2 , SO4 A:15 , G B:11 , G B:12 , G B:13BINDING SITE FOR RESIDUE NCO B 15
4AC4SOFTWAREC A:2 , NCO B:15BINDING SITE FOR RESIDUE SO4 A 15

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GS8)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:13
                                            
                  3gs8 A  1 UCCCAGUCCACCG 13
                                    10   


Chain B from PDB  Type:RNA  Length:12
                                           
                  3gs8 B  2 CGGUGAGAAGGG 13
                                    11  


Chain C from PDB  Type:RNA  Length:17
                                                
                  3gs8 C 15 GGCAGAGAAACACACGA 31
                                    24       


Chain D from PDB  Type:RNA  Length:19
                                                  
                  3gs8 D 31 UCGUGGUACAUUACCUGCC 49
                                    40
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3gs1 3gs5