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(-) Description

Title :  AMIDE LINKED RNA
 
Authors :  P. S. Pallan, M. Egli
Date :  18 Dec 13  (Deposition) - 09 Jul 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Modified Rna, Rna Structure, Amide Rna, Amide Internucleoside Linkage, Modified Nucleoside, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Mutisya, C. Selvam, B. D. Lunstad, P. S. Pallan, A. Haas, D. Leake, M. Egli, E. Rozners
Amides Are Excellent Mimics Of Phosphate Internucleoside Linkages And Are Well Tolerated In Short Interfering Rnas.
Nucleic Acids Res. V. 42 6542 2014
PubMed-ID: 24813446  |  Reference-DOI: 10.1093/NAR/GKU235

(-) Compounds

Molecule 1 - AMIDE LINKED RNA
    Chains: A, B, C, D
    Engineered: YES
    Other Details: SHORT NA STRANDS UGAGC(URU)CGGCUC, WHERE URU REPRESENTS THE AMIDE LINKED RESIDUE
    Other Details - Source: CHEMICALLY SYNTHESIZED MODIFIED RIBO NUCLEIC ACID
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1SR2Ligand/IonSTRONTIUM ION
2URU4Mod. Nucleotide((2S,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3-(2- ((((2R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)- 3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL)AMINO)-2-OXOETHYL)-4- HYDROXYTETRAHYDROFURAN-2-YL)METHYLPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SR-1Ligand/IonSTRONTIUM ION
2URU2Mod. Nucleotide((2S,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3-(2- ((((2R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)- 3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL)AMINO)-2-OXOETHYL)-4- HYDROXYTETRAHYDROFURAN-2-YL)METHYLPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SR-1Ligand/IonSTRONTIUM ION
2URU2Mod. Nucleotide((2S,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3-(2- ((((2R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)- 3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL)AMINO)-2-OXOETHYL)-4- HYDROXYTETRAHYDROFURAN-2-YL)METHYLPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:113 , HOH A:815 , HOH A:817 , HOH A:840 , HOH A:866BINDING SITE FOR RESIDUE SR A 701
2AC2SOFTWAREG A:109 , G A:110 , HOH A:805 , HOH A:811 , HOH A:814 , HOH A:821 , HOH A:835 , HOH A:838BINDING SITE FOR RESIDUE SR A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O41)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O41)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O41)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4O41)

(-) Sequences/Alignments

Asymmetric 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    
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Chain A from PDB  Type:RNA  Length:11
                                           
                 4o41 A 102 GAGCxCGGCUC 113
                                || 112 
                                ||     
                              106-URU  
                               108     


Chain B from PDB  Type:RNA  Length:12
                                            
                 4o41 B 201 UGAGCxCGGCUC 213
                                 ||211  
                               206-URU  
                                208     


Chain C from PDB  Type:RNA  Length:11
                                           
                 4o41 C 302 GAGCxCGGCUC 313
                                || 312 
                              306-URU  
                               308     


Chain D from PDB  Type:RNA  Length:11
                                           
                 4o41 D 402 GAGCxCGGCUC 413
                                || 412 
                              406-URU  
                               408
   Legend:   → Mismatch (orange background)
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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 4O41)

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(-) Gene Ontology  (0, 0)

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