SMTL ID : 3irw.1

Structure of a c-di-GMP riboswitch from V. cholerae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-functional Binders)

C2E.1: 15 residues within 4Å: Chain B: G.7, A.9, C.10, A.11, G.12, G.13, G.14, C.39, A.40, A.41, A.42, C.86, C.87 Ligands: IRI.4, MG.12 No protein-ligand interaction detected (PLIP)

9 x IRI: IRIDIUM HEXAMMINE ION(Non-functional Binders)

IRI.2: 5 residues within 4Å: Chain B: C.39, A.40, A.41, A.42, G.79 No protein-ligand interaction detected (PLIP) IRI.3: 8 residues within 4Å: Chain B: U.46, C.48, G.49, G.50, C.51, G.74, U.75 Ligands: IRI.10 No protein-ligand interaction detected (PLIP) IRI.4: 5 residues within 4Å: Chain B: C.10, A.11, G.12, G.13 Ligands: C2E.1 No protein-ligand interaction detected (PLIP) IRI.5: 9 residues within 4Å: Chain B: C.44, C.45, A.76, G.77, G.79, G.80, G.81, G.82 Ligands: IRI.8 No protein-ligand interaction detected (PLIP) IRI.6: 6 residues within 4Å: Chain B: G.1, G.2, U.3, C.4, U.90, G.91 No protein-ligand interaction detected (PLIP) IRI.7: 3 residues within 4Å: Chain B: C.24, G.25, A.27 No protein-ligand interaction detected (PLIP) IRI.8: 5 residues within 4Å: Chain B: G.80, G.81, G.82, U.83 Ligands: IRI.5 No protein-ligand interaction detected (PLIP) IRI.9: 5 residues within 4Å: Chain B: A.17, A.18, A.30, G.77, C.78 No protein-ligand interaction detected (PLIP) IRI.10: 5 residues within 4Å: Chain B: U.46, A.72, G.73, G.74 Ligands: IRI.3 No protein-ligand interaction detected (PLIP)

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

MG.11: 4 residues within 4Å: Chain B: C.15, A.16, G.38, A.42 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: C.8 Ligands: C2E.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, K.D. et al., Structural basis of ligand binding by a c-di-GMP riboswitch. Nat.Struct.Mol.Biol. (2009)

Release Date

2009-11-10

Peptides

U1 small nuclear ribonucleoprotein A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

U1 small nuclear ribonucleoprotein A

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