SMTL ID : 4oaz.1

BldD CTD-c-di-GMP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

4 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-covalent)

C2E.1: 15 residues within 4Å: Chain A: K.9, R.39, S.48, I.49, R.50, Q.51 Chain B: I.35, Q.38, R.39, I.49, R.50, D.53 Ligands: C2E.2, C2E.3, C2E.4 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.39, B:R.39, B:R.50, B:R.50, A:R.50, A:R.50, A:Q.51 Water bridges: B:R.39, A:K.9 Salt bridges: B:R.50, B:D.53, A:K.9 pi-Cation interactions: B:R.50 C2E.2: 14 residues within 4Å: Chain A: K.9, R.39, D.41, N.43, V.46, L.47, S.48 Chain B: R.39, G.40, D.41, S.48 Ligands: C2E.1, C2E.3, C2E.4 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:R.39, A:R.39, A:N.43, A:N.43, A:S.48 Water bridges: A:K.9, A:K.9 Salt bridges: A:K.9, A:D.41 C2E.3: 15 residues within 4Å: Chain A: I.35, Q.38, R.39, I.49, R.50, D.53 Chain B: K.9, R.39, S.48, I.49, R.50, Q.51 Ligands: C2E.1, C2E.2, C2E.4 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:R.39, B:S.48, B:R.50, B:R.50, B:Q.51, A:R.39, A:R.39, A:R.50, A:R.50, A:R.50 Salt bridges: B:K.9, A:R.50, A:D.53 pi-Cation interactions: B:R.39, A:R.50 Water bridges: A:R.39 C2E.4: 15 residues within 4Å: Chain A: R.39, G.40, D.41, N.43, S.48 Chain B: K.9, R.39, D.41, N.43, V.46, L.47, S.48 Ligands: C2E.1, C2E.2, C2E.3 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.39, B:S.48, A:R.39, A:N.43 Salt bridges: B:K.9, B:D.41, A:D.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tschowri, N. et al., Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development. Cell(Cambridge,Mass.) (2014)

Release Date

2014-11-19

Peptides

Putative DNA-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
A

Putative DNA-binding protein