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(-) Description

Title :  ATOMIC RESOLUTION CRYSTAL STRUCTURE OF A VIRAL RNA PSEUDOKNOT
 
Authors :  M. Egli, G. Minasov, L. Su, A. Rich
Date :  25 Feb 02  (Deposition) - 22 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Pseudoknot, Frameshifting, Atomic Resolution, Viral Rna, Metal Ions, Flexibility (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Egli, G. Minasov, L. Su, A. Rich
Metal Ions And Flexibility In A Viral Rna Pseudoknot At Atomic Resolution.
Proc. Natl. Acad. Sci. Usa V. 99 4302 2002
PubMed-ID: 11904368  |  Reference-DOI: 10.1073/PNAS.062055599
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA PSEUDOKNOT
    Chains: A
    Engineered: YES
    Other Details: METAL IONS IN A RNA PSEUDOKNOT
    Other Details - Source: RNA SEQUENCE TAKEN FROM BEET WESTERN YELLOW VIRUS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2K1Ligand/IonPOTASSIUM ION
3MG6Ligand/IonMAGNESIUM ION
4NA3Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGTP A:1 , G A:2 , HOH A:30 , HOH A:31 , HOH A:32 , HOH A:33BINDING SITE FOR RESIDUE MG A 29
02AC2SOFTWAREGTP A:1 , G A:19 , HOH A:35 , HOH A:36 , HOH A:37 , MG A:59BINDING SITE FOR RESIDUE MG A 34
03AC3SOFTWAREHOH A:39 , HOH A:40 , HOH A:41 , HOH A:42 , HOH A:43 , HOH A:44BINDING SITE FOR RESIDUE MG A 38
04AC4SOFTWAREHOH A:46 , HOH A:47 , HOH A:48 , HOH A:49 , HOH A:50 , HOH A:51BINDING SITE FOR RESIDUE MG A 45
05AC5SOFTWAREHOH A:53 , HOH A:54 , HOH A:55 , HOH A:56 , HOH A:57 , HOH A:58BINDING SITE FOR RESIDUE MG A 52
06AC6SOFTWAREGTP A:1 , G A:19 , MG A:34 , HOH A:35 , HOH A:36 , HOH A:60BINDING SITE FOR RESIDUE MG A 59
07AC7SOFTWAREG A:16 , A A:21 , HOH A:92BINDING SITE FOR RESIDUE NA A 61
08AC8SOFTWAREC A:3 , G A:4 , G A:18 , HOH A:101BINDING SITE FOR RESIDUE NA A 62
09AC9SOFTWAREC A:5 , G A:6 , A A:21 , HOH A:79BINDING SITE FOR RESIDUE NA A 63
10BC1SOFTWAREGTP A:1 , G A:2 , HOH A:66 , HOH A:102BINDING SITE FOR RESIDUE K A 64

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L2X)

(-) Exons   (0, 0)

(no "Exon" information available for 1L2X)

(-) 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    
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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:28
                                                           
                  1l2x A  1 gGCGCGGCACCGUCCGCGGAACAAACGG 28
                            |       10        20        
                            |                           
                            1-GTP
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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 1L2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1L2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1L2X)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

1l3d LOW RESOLUTION CRYSTAL STRUCTURE OF A VIRAL RNA PSEUDOKNOT
437d 437D IS THE SAME RNA PSEUDOKNOT STRUCTURE AT 1.6 ANGSTROM RESOLUTION