SMTL ID : 4w90.1

Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.12 Å

Oligo State

monomer

Ligands

2 x 2BA: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide(Non-functional Binders)

2BA.1: 14 residues within 4Å: Chain B: A.9, G.25, G.26, G.27, G.28, G.60, G.61, U.62, G.63, C.95, C.96, A.100, C.109, G.110 No protein-ligand interaction detected (PLIP) 2BA.2: 14 residues within 4Å: Chain B: G.5, C.6, U.7, U.8, A.64, G.80, G.81, C.82, G.83, C.89, C.90, G.114, C.115, G.116 No protein-ligand interaction detected (PLIP)

5 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 2 residues within 4Å: Chain B: A.30, G.101 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: U.7, C.82 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: G.27, U.62 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: G.79, G.80 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain B: G.28, G.29, A.100, G.101, C.102, U.103 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, C.P. et al., Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. Embo J. (2014)

Release Date

2014-10-15

Peptides

U1 small nuclear ribonucleoprotein A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

U1 small nuclear ribonucleoprotein A

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