SMTL ID : 7v0r.1

Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -ppcpG(2 ,5 )pA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

2 x OKX: [(2~{R},3~{R},4~{R},5~{R})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid(Non-covalent)

OKX.1: 21 residues within 4Å: Chain A: G.55, S.56, E.59, 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.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.56, A:S.56, A:R.221, A:S.223, A:S.223, A:S.225, A:S.277, A:S.277, A:Y.278 Water bridges: A:Y.57 Salt bridges: A:K.62, A:K.259 OKX.5: 22 residues within 4Å: Chain B: G.55, S.56, E.59, E.68, D.70, G.147, S.148, P.149, A.150, D.164, I.166, K.207, R.221, L.222, S.223, S.225, K.259, C.276, S.277, Y.278 Ligands: MG.6, MG.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.56, B:S.56, B:G.147, B:R.221, B:R.221, B:L.222, B:S.277, B:S.277, B:Y.278 Water bridges: B:Y.57 Salt bridges: B:K.207, B:K.259

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.68, D.70 Ligands: OKX.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.68, A:D.70, H2O.1 MG.3: 5 residues within 4Å: Chain A: E.68, D.70, D.164 Ligands: OKX.1, MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.68, A:E.68, A:D.70, A:D.164 MG.6: 4 residues within 4Å: Chain B: E.68, D.70 Ligands: OKX.5, MG.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.68, B:D.70, H2O.1 MG.7: 5 residues within 4Å: Chain B: E.68, D.70, D.164 Ligands: OKX.5, MG.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.68, B:E.68, B:D.70, B:D.164

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.8: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, S. et al., Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -ppcpG(2 ,5 )pA. To Be Published

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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