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(-) Description

Title :  SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI K-T-7
 
Authors :  P. Daldrop, D. M. J. Lilley
Date :  07 Aug 12  (Deposition) - 30 Jan 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rna, Riboswitch, K-Turn (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Daldrop, D. M. J. Lilley
The Plasticity Of A Structural Motif In Rna: Structural Polymorphism Of A Kink Turn As A Function Of Its Environment.
Rna V. 19 357 2013
PubMed-ID: 23325110  |  Reference-DOI: 10.1261/RNA.036657.112

(-) Compounds

Molecule 1 - SAM-I RIBOSWITCH
    ChainsA
    FragmentAPTAMER DOMAIN, RESIDUES 1-94
    Organism ScientificTHERMOANAEROBACTER TENGCONGENSIS
    Organism Taxid119072
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1BA12Ligand/IonBARIUM ION
2K7Ligand/IonPOTASSIUM ION
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BA-1Ligand/IonBARIUM ION
2K-1Ligand/IonPOTASSIUM ION
3SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREU A:7 , C A:8 , A A:10 , G A:11 , A A:45 , A A:46 , C A:47 , U A:57 , G A:58 , C A:59 , U A:88 , G A:89BINDING SITE FOR RESIDUE SAM A1095
02AC2SOFTWAREG A:27 , G A:28BINDING SITE FOR RESIDUE BA A1096
03AC3SOFTWAREA A:10 , G A:11 , A A:62BINDING SITE FOR RESIDUE K A1097
04AC4SOFTWAREG A:50BINDING SITE FOR RESIDUE K A1098
05AC5SOFTWAREU A:64 , U A:67BINDING SITE FOR RESIDUE BA A1099
06AC6SOFTWAREU A:81 , G A:82BINDING SITE FOR RESIDUE K A1100
07AC7SOFTWAREG A:11 , U A:64BINDING SITE FOR RESIDUE BA A1101
08AC8SOFTWAREA A:70 , G A:71 , G A:79 , U A:80BINDING SITE FOR RESIDUE K A1102
09AC9SOFTWAREA A:85 , G A:86BINDING SITE FOR RESIDUE K A1103
10BC1SOFTWAREG A:15 , G A:16BINDING SITE FOR RESIDUE BA A1104
11BC2SOFTWAREG A:74BINDING SITE FOR RESIDUE BA A1105
12BC3SOFTWAREG A:1 , BA A:1110BINDING SITE FOR RESIDUE BA A1106
13BC4SOFTWAREG A:18BINDING SITE FOR RESIDUE BA A1107
14BC5SOFTWAREU A:88BINDING SITE FOR RESIDUE BA A1108
15BC6SOFTWAREG A:32BINDING SITE FOR RESIDUE BA A1109
16BC7SOFTWAREG A:1 , BA A:1106BINDING SITE FOR RESIDUE BA A1110
17BC8SOFTWAREG A:94BINDING SITE FOR RESIDUE BA A1112
18BC9SOFTWAREG A:56BINDING SITE FOR RESIDUE K A1113
19CC1SOFTWAREG A:13BINDING SITE FOR RESIDUE K A1114

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B5R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B5R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B5R)

(-) Exons   (0, 0)

(no "Exon" information available for 4B5R)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:RNA  Length:94
                                                                                                                             
                  4b5r A  1 GGCUUAUCAAGAGAGGGGGAGCGACUGGCGCGAAGAACCCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCG 94
                                    10        20        30        40        50        60        70        80        90    

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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 4B5R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B5R)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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