SMTL ID : 8ad6.1

Structure of DarB bound to c-di-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

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-covalent)

2BA.1: 15 residues within 4Å: Chain A: K.23, V.24, A.25, Y.45, T.46, A.47, I.48, G.114, F.115, I.128, T.130, R.131, R.132 Chain B: N.112, R.131 20 PLIP interactions: 6 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:R.131, B:R.131, A:K.23, A:A.25, A:Y.45, A:T.46, A:T.46, A:A.47, A:R.132 Water bridges: B:T.46, B:T.46, B:T.46, A:Y.45, A:T.46, A:T.46, A:T.130, A:T.130 Salt bridges: B:R.131 pi-Stacking: A:Y.45, A:Y.45 2BA.2: 16 residues within 4Å: Chain A: I.111, N.112, R.131 Chain B: K.23, V.24, A.25, Y.45, T.46, A.47, I.48, G.114, F.115, I.128, T.130, R.131, R.132 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.23, B:A.25, B:Y.45, B:Y.45, B:T.46, B:A.47, B:R.131, B:R.132, A:I.111, A:R.131, A:R.131 Water bridges: B:T.46, B:T.46 pi-Stacking: B:Y.45, B:Y.45 Salt bridges: A:R.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Pino, A. et al., Structure of DarB bound to c-di-AMP. To Be Published

Release Date

2023-07-19

Peptides

CBS domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CBS domain-containing protein

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