SMTL ID : 6yja.1

DarB fom B. subtilis in complex with c-di-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: 16 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: I.111, N.112, R.131 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.23, A:A.25, A:T.46, A:A.47, A:R.132, B:I.111, B:R.131, B:R.131 Water bridges: A:T.43, A:Y.45, A:Y.45, A:T.46, A:T.46 pi-Stacking: A:Y.45, A:Y.45 Salt bridges: B:R.131 2BA.5: 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 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:I.111, A:R.131, B:K.23, B:A.25, B:T.46, B:T.46, B:A.47, B:R.132 Water bridges: A:T.46, B:T.43, B:Y.45, B:Y.45, B:T.46, B:T.46, B:T.130 Salt bridges: A:R.131 pi-Stacking: B:Y.45, B:Y.45

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: K.105, G.108, M.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.105

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: D.93 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.93, A:D.93, H2O.1, H2O.3

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.131 Chain B: R.131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heidemann, J.L. et al., DarB from B. subtilis. To Be Published

Release Date

2021-04-14

Peptides

CBS domain-containing protein YkuL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CBS domain-containing protein YkuL

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