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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH (4-(1,2,3-THIADIAZOL-4-YL)PHENYL)METHANAMINE
 
Authors :  K. D. Warner, P. Homan, K. M. Weeks, A. G. Smith, C. Abell, A. R. Ferre-D'A
Date :  10 Dec 13  (Deposition) - 04 Jun 14  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Fragment-Based Drug Discovery, Riboswitch, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. D. Warner, P. Homan, K. M. Weeks, A. G. Smith, C. Abell, A. R. Ferre-D'Amare
Validating Fragment-Based Drug Discovery For Biological Rnas: Lead Fragments Bind And Remodel The Tpp Riboswitch Specifically.
Chem. Biol. V. 21 591 2014
PubMed-ID: 24768306  |  Reference-DOI: 10.1016/J.CHEMBIOL.2014.03.007

(-) Compounds

Molecule 1 - THIM TPP RIBOSWITCH
    ChainsA
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
12QC1Ligand/Ion1-[4-(1,2,3-THIADIAZOL-4-YL)PHENYL]METHANAMINE
2A231Mod. NucleotideADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
3MG9Ligand/IonMAGNESIUM ION
4MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:19 , U A:39 , G A:40 , G A:42 , A A:43 , C A:73 , C A:74BINDING SITE FOR RESIDUE 2QC A 101
02AC2SOFTWAREG A:21 , C A:38 , U A:39 , U A:71 , C A:73BINDING SITE FOR RESIDUE MG A 102
03AC3SOFTWAREA A:69 , A23 A:91BINDING SITE FOR RESIDUE MG A 103
04AC4SOFTWAREA A:80 , G A:81BINDING SITE FOR RESIDUE MN A 104
05AC5SOFTWAREG A:66BINDING SITE FOR RESIDUE MG A 105
06AC6SOFTWAREG A:18 , HOH A:202BINDING SITE FOR RESIDUE MG A 106
07AC7SOFTWAREA A:69 , A23 A:91BINDING SITE FOR RESIDUE MG A 107
08AC8SOFTWAREG A:66 , A A:67 , HOH A:204BINDING SITE FOR RESIDUE MG A 108
09AC9SOFTWAREA A:35 , G A:36 , HOH A:205BINDING SITE FOR RESIDUE MG A 109
10BC1SOFTWAREC A:63 , U A:64 , HOH A:203BINDING SITE FOR RESIDUE MN A 110
11BC2SOFTWAREA A:41BINDING SITE FOR RESIDUE MG A 111
12BC3SOFTWAREU A:59 , G A:60 , G A:72 , G A:78BINDING SITE FOR RESIDUE MN A 112
13BC4SOFTWAREA A:85 , G A:86BINDING SITE FOR RESIDUE MG A 113
14BC5SOFTWAREG A:40 , HOH A:206 , HOH A:207 , HOH A:208 , HOH A:209BINDING SITE FOR RESIDUE MN A 114

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4NYB)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:DNA/RNA  Length:80
                                                                                                               
                  4nyb A  9 GCGACUCGGGGUGCCCUUCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCGCa 91
                                    18       |31        41        51        61        71        81        91
                                            26|                                                           91-A23
                                             30                                                             

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NYB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) 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

4nya CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH 5-(AZIDOMETHYL)-2-METHYLPYRIMIDIN-4-AMINE
4nyc CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH THIENO[2,3-B]PYRAZIN-7-AMINE
4nyd CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH HYPOXANTHINE
4nyg CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH THIAMINE