3D2V - JenaLib

Title :   STRUCTURE OF THE EUKARYOTIC TPP-SPECIFIC RIBOSWITCH BOUND TO THE ANTIBACTERIAL COMPOUND PYRITHIAMINE PYROPHOSPHATE

Authors :   S. Thore, C. Frick, N. Ban

Date :   09 May 08 (Deposition) - 01 Jul 08 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Rna, Riboswitch, Antibiotic, Thiamine Pyrophosphate, Pyrithiamine Pyrophosphate, Complex (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	PYI	2	Ligand/Ion	1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PYI	1	Ligand/Ion	1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PYI	1	Ligand/Ion	1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PYI A:84 , HOH A:94 , HOH A:96 , HOH A:98 , HOH A:341	BINDING SITE FOR RESIDUE MG A 78
02	AC2	SOFTWARE	C A:51 , A A:52 , HOH A:88 , HOH A:108 , HOH A:345 , HOH B:98	BINDING SITE FOR RESIDUE MG A 79
03	AC3	SOFTWARE	U A:41 , G A:42 , C A:65 , HOH A:167 , HOH A:332	BINDING SITE FOR RESIDUE MG A 80
04	AC4	SOFTWARE	G A:48 , G A:66 , PYI A:84 , HOH A:85 , HOH A:89 , HOH A:339	BINDING SITE FOR RESIDUE MG A 81
05	AC5	SOFTWARE	A A:29 , HOH A:114 , HOH A:151 , HOH A:208 , HOH A:319 , HOH A:321	BINDING SITE FOR RESIDUE MG A 82
06	AC6	SOFTWARE	G A:48 , HOH A:107 , HOH A:258 , HOH B:118 , HOH B:296	BINDING SITE FOR RESIDUE MG A 83
07	AC7	SOFTWARE	HOH A:102 , C B:51 , A B:52 , HOH B:88 , HOH B:111 , HOH B:300	BINDING SITE FOR RESIDUE MG B 78
08	AC8	SOFTWARE	PYI B:82 , HOH B:87 , HOH B:180 , HOH B:315 , HOH B:316	BINDING SITE FOR RESIDUE MG B 79
09	AC9	SOFTWARE	G B:48 , G B:66 , PYI B:82 , HOH B:83 , HOH B:89 , HOH B:314	BINDING SITE FOR RESIDUE MG B 80
10	BC1	SOFTWARE	HOH A:236 , A B:29 , HOH B:90 , HOH B:127 , HOH B:172 , HOH B:182	BINDING SITE FOR RESIDUE MG B 81
11	BC2	SOFTWARE	G A:11 , U A:12 , G A:28 , G A:30 , A A:31 , A A:43 , C A:45 , G A:60 , C A:61 , C A:65 , G A:66 , MG A:78 , MG A:81 , HOH A:93 , HOH A:94 , HOH A:101 , HOH A:142 , HOH A:144 , HOH A:339 , HOH A:341	BINDING SITE FOR RESIDUE PYI A 84
12	BC3	SOFTWARE	G B:11 , U B:12 , G B:28 , G B:30 , A B:31 , A B:43 , C B:45 , G B:60 , C B:61 , C B:65 , G B:66 , MG B:79 , MG B:80 , HOH B:83 , HOH B:87 , HOH B:96 , HOH B:104 , HOH B:120 , HOH B:135 , HOH B:153 , HOH B:162 , HOH B:314 , HOH B:315 , HOH B:331	BINDING SITE FOR RESIDUE PYI B 82

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

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:RNA  Length:77
                                                                                                            
                  3d2v A  1 GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC 77
                                    10        20        30        40        50        60        70

Chain B from PDB  Type:RNA  Length:77
                                                                                                            
                  3d2v B  1 GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC 77
                                    10        20        30        40        50        60        70

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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