SMTL ID : 6yj9.1

DarB in complex with 3'3'cGAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

4 x 4BW: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one(Non-covalent)

4BW.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 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.23, A:A.25, A:T.46, A:A.47, A:R.131, A:R.132, B:N.112, B:R.131, B:R.131 Water bridges: A:Y.45, A:Y.45, B:T.46, B:N.112 pi-Stacking: A:Y.45, A:Y.45 Salt bridges: B:R.131 4BW.2: 5 residues within 4Å: Chain A: N.112 Chain B: Y.45, R.132 Ligands: 4BW.3, 4BW.4 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.112, B:Y.45, B:Y.45, B:Y.45 Water bridges: A:N.113, A:N.113 4BW.3: 17 residues within 4Å: Chain A: 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 Ligands: 4BW.2, 4BW.4 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.23, B:A.25, B:T.46, B:A.47, B:R.132, A:N.112, A:R.131 Water bridges: B:T.46, B:T.46 pi-Stacking: B:Y.45, B:Y.45 Salt bridges: A:R.131 4BW.4: 10 residues within 4Å: Chain B: F.17, M.18, I.19, E.20, K.23, Y.45, R.132, K.136 Ligands: 4BW.2, 4BW.3 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:F.17, B:M.18, B:E.20, B:Y.45, B:K.136 Water bridges: B:K.23, B:R.132, B:R.132, B:R.132, B:R.132, B:K.136 Salt bridges: B:K.23, B:R.132, B:K.136

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

CL.5: 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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