3D2G - JenaLib

Title :   STRUCTURAL BASIS OF THIAMINE PYROPHOSPHATE ANALOGUES BINDING TO THE EUKARYOTIC RIBOSWITCH

Authors :   S. Thore

Date :   08 May 08 (Deposition) - 01 Jul 08 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Rna, Riboswitch, Tpp, Thiamine Analogues, Antibiotics, Arabidopsis Thaliana, Eukaryote (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Thore, C. Frick, N. Ban
Structural Basis Of Thiamine Pyrophosphate Analogues Bindin To The Eukaryotic Riboswitch
J. Am. Chem. Soc. V. 130 8116 2008
PubMed-ID: 18533652 | Reference-DOI: 10.1021/JA801708E

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MG	10	Ligand/Ion	MAGNESIUM ION
2	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TPP	1	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TPP	1	Ligand/Ion	THIAMINE DIPHOSPHATE

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G B:48 , G B:66 , TPP B:83 , HOH B:84 , HOH B:85 , HOH B:86	BINDING SITE FOR RESIDUE MG B 78
02	AC2	SOFTWARE	HOH A:84 , C B:51 , A B:52 , HOH B:87 , HOH B:88 , HOH B:89	BINDING SITE FOR RESIDUE MG B 79
03	AC3	SOFTWARE	TPP A:83 , HOH A:89 , HOH A:90 , HOH A:91 , HOH A:92	BINDING SITE FOR RESIDUE MG A 78
04	AC4	SOFTWARE	G A:48 , G A:66 , TPP A:83 , HOH A:93 , HOH A:94 , HOH A:95	BINDING SITE FOR RESIDUE MG A 79
05	AC5	SOFTWARE	C A:51 , A A:52 , HOH A:96 , HOH A:97 , HOH A:98 , HOH B:90	BINDING SITE FOR RESIDUE MG A 80
06	AC6	SOFTWARE	U B:63 , TPP B:83 , HOH B:91 , HOH B:92 , HOH B:93 , HOH B:94	BINDING SITE FOR RESIDUE MG B 80
07	AC7	SOFTWARE	G A:42 , C A:65 , C A:67 , HOH A:85 , HOH A:86 , HOH A:87 , HOH A:88	BINDING SITE FOR RESIDUE MG A 82
08	AC8	SOFTWARE	A A:29 , HOH A:99 , HOH A:100 , HOH A:101 , HOH A:132 , HOH A:158	BINDING SITE FOR RESIDUE MG A 81
09	AC9	SOFTWARE	A B:29 , HOH B:102 , HOH B:104	BINDING SITE FOR RESIDUE MG B 81
10	BC1	SOFTWARE	C B:67 , HOH B:95 , HOH B:96	BINDING SITE FOR RESIDUE MG B 82
11	BC2	SOFTWARE	G A:11 , G A:28 , G A:30 , A A:31 , C A:45 , G A:60 , C A:61 , C A:65 , G A:66 , MG A:78 , MG A:79 , HOH A:89 , HOH A:91 , HOH A:92 , HOH A:93 , HOH A:95 , HOH A:119	BINDING SITE FOR RESIDUE TPP A 83
12	BC3	SOFTWARE	G B:11 , U B:12 , G B:28 , G B:30 , A B:31 , C B:45 , G B:60 , C B:61 , C B:65 , G B:66 , MG B:78 , MG B:80 , HOH B:84 , HOH B:85 , HOH B:93 , HOH B:94 , HOH B:98 , HOH B:112	BINDING SITE FOR RESIDUE TPP B 83

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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Chain A from PDB  Type:RNA  Length:77
                                                                                                            
                  3d2g A  1 GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC 77
                                    10        20        30        40        50        60        70

Chain B from PDB  Type:RNA  Length:77
                                                                                                            
                  3d2g B  1 GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC 77
                                    10        20        30        40        50        60        70

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Classification and Annotation

SCOP Domains (0, 0)

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