SMTL ID : 8eae.1

Structure of Ternary Complex of cGAS with dsDNA and Bound 5-pppG(2,5)pI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-dimer

Ligands

2 x VLO: [[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

VLO.1: 19 residues within 4Å: Chain A: G.55, S.56, E.68, D.70, M.72, G.147, S.148, P.149, A.150, D.164, I.166, R.221, S.223, S.225, K.259, C.276, S.277, Y.278 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.56, A:S.56, A:S.56, A:E.68, A:D.164, A:R.221, A:R.221, A:S.223, A:S.223, A:S.225, A:S.277, A:Y.278 Water bridges: A:Y.57, A:K.62, A:E.228, A:Y.278, A:K.281 Salt bridges: A:K.259, A:K.259 pi-Stacking: A:Y.278 VLO.4: 19 residues within 4Å: Chain B: T.54, G.55, S.56, E.68, D.70, S.148, P.149, A.150, D.164, I.166, K.207, R.221, S.223, S.225, K.259, C.276, S.277, Y.278 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.56, B:S.56, B:S.56, B:D.164, B:R.221, B:S.223, B:S.225, B:S.225, B:S.277, B:Y.278 Water bridges: B:Y.57 Salt bridges: B:R.221, B:K.259, B:K.259 pi-Stacking: B:Y.278 pi-Cation interactions: B:Y.278

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.235, C.241, C.242, C.249 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.235, A:C.241, A:C.242, A:C.249 ZN.5: 4 residues within 4Å: Chain B: H.235, C.241, C.242, C.249 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.235, B:C.241, B:C.242, B:C.249

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.56, E.68, D.70 Ligands: VLO.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.68, A:D.70, H2O.1 MG.6: 3 residues within 4Å: Chain B: E.68, D.70 Ligands: VLO.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.68, B:D.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, S. et al., The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS. Nat Commun (2024)

Release Date

2023-10-25

Peptides

Cyclic GMP-AMP synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Cyclic GMP-AMP synthase

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