SMTL ID : 9c8n.1

Crystal Structure of human cyclic GMP-AMP synthase in complex with AMPPNP and compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x 01: 1-[(1S)-6,7-dichloro-1-methyl-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl]-2-methoxyethan-1-one

01.1: 14 residues within 4Å: Chain A: E.70, D.72, S.150, P.151, A.152, D.164, T.166, V.205, K.207, R.221, L.222, S.223 Ligands: MG.4, ANP.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.151, A:A.152, A:V.205 Water bridges: A:K.207, A:K.207 Halogen bonds: A:L.222

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: L.19, I.24, Y.59, H.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.59 GOL.3: 6 residues within 4Å: Chain A: H.289, Y.315, C.319, K.324, L.325, E.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.324, A:E.326 Water bridges: A:E.326

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: E.70, D.72, D.164 Ligands: 01.1, MG.5, ANP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.70, A:D.72, A:D.164 MG.5: 5 residues within 4Å: Chain A: S.58, E.70, D.72 Ligands: MG.4, ANP.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.70, A:D.72, H2O.3

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 15 residues within 4Å: Chain A: G.57, S.58, K.64, E.70, D.72, R.221, S.225, E.228, K.259, S.280, Y.281, K.284 Ligands: 01.1, MG.4, MG.5 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:S.58, A:S.58, A:S.58, A:E.70, A:K.259, A:S.280, A:K.284, A:K.284 Water bridges: A:Y.59, A:Y.59, A:E.70, A:E.70, A:R.221, A:R.221, A:S.225, A:S.225, A:K.259, A:K.259, A:K.259, A:S.279, A:S.279, A:Y.281 pi-Stacking: A:Y.281, A:Y.281

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skeldon, A.M. et al., Structural insight into the cGAS active site explains differences between therapeutically relevant species. Commun Chem (2025)

Release Date

2025-04-02

Peptides

Cyclic GMP-AMP synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclic GMP-AMP synthase

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