SMTL ID : 7uzr.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

OKR.1: 15 residues within 4Å: Chain A: G.55, S.56, K.62, E.68, D.70, K.145, R.221, K.259, K.266, F.275, C.276, S.277, Y.278 Ligands: MN.3, MN.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.56, A:S.56, A:S.56, A:R.221, A:K.266, A:S.277, A:S.277, A:S.277, A:S.277, A:Y.278 Water bridges: A:Y.57, A:K.259, A:K.259 Salt bridges: A:E.68, A:K.259, A:K.259 pi-Stacking: A:Y.278 OKR.5: 16 residues within 4Å: Chain B: G.55, S.56, K.62, E.68, D.70, K.145, K.207, R.221, K.259, K.266, F.275, C.276, S.277, Y.278 Ligands: MN.7, MN.8 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.56, B:S.56, B:S.56, B:K.145, B:R.221, B:K.266, B:S.277, B:S.277, B:S.277, B:S.277, B:Y.278 Water bridges: B:Y.57, B:Y.57 Salt bridges: B:E.68, B:K.207, B:K.259, B:K.259 pi-Stacking: B:Y.278 pi-Cation interactions: B:K.207

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.6: 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

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 5 residues within 4Å: Chain A: E.68, D.70, D.164 Ligands: OKR.1, MN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.68, A:D.70, A:D.164 MN.4: 5 residues within 4Å: Chain A: S.56, E.68, D.70 Ligands: OKR.1, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.68, A:D.70, H2O.1 MN.7: 5 residues within 4Å: Chain B: E.68, D.70, D.164 Ligands: OKR.5, MN.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.68, B:D.70, B:D.164 MN.8: 5 residues within 4Å: Chain B: S.56, E.68, D.70 Ligands: OKR.5, MN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.68, B:D.70, H2O.1

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

2023-05-10

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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