SMTL ID : 7fuj.1

Crystal Structure of human cyclic GMP-AMP synthase in complex with (Z)-2-cyano-N-[4-(3-fluorophenyl)-5-methylsulfonylpyrimidin-2-yl]-3-hydroxy-3-(5-methyl-1,2-oxazol-4-yl)prop-2-enamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.230, C.236, C.237, C.244 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.230, A:C.236, A:C.237, A:C.244

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.53, E.65, D.67 Ligands: MG.3, ATP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.65, A:D.67, H2O.2 MG.3: 5 residues within 4Å: Chain A: E.65, D.67, D.159 Ligands: MG.2, ATP.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.65, A:D.67, A:D.159, H2O.4, H2O.5

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 15 residues within 4Å: Chain A: G.52, S.53, E.65, D.67, R.216, S.220, E.223, K.254, S.275, Y.276, K.279 Ligands: MG.2, MG.3, YR6.6, EDO.8 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.53, A:S.53, A:E.65, A:R.216, A:S.220, A:S.275, A:K.279, A:K.279 Water bridges: A:Y.54, A:Y.54, A:K.59, A:K.59, A:E.65, A:K.254, A:K.254, A:S.274, A:S.274, A:Y.276 Salt bridges: A:K.254, A:K.254 pi-Stacking: A:Y.276, A:Y.276

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: E.10, K.13, R.16 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.13, A:R.16 SO4.10: 4 residues within 4Å: Chain A: L.227, N.228, H.230, K.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.228 Salt bridges: A:H.230, A:K.247 SO4.11: 4 residues within 4Å: Chain A: K.232, Q.291, D.292, S.293 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.292, A:D.292, A:S.293 Water bridges: A:Q.291, A:S.293 SO4.12: 1 residues within 4Å: Chain A: S.83 No protein-ligand interaction detected (PLIP) SO4.13: 3 residues within 4Å: Chain A: N.50, Y.55, K.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.50 Water bridges: A:N.50, A:K.224 Salt bridges: A:K.224

1 x YR6: (2Z)-2-cyano-N-[(4P)-4-(3-fluorophenyl)-5-(methanesulfonyl)pyrimidin-2-yl]-3-hydroxy-3-(5-methyl-1,2-oxazol-4-yl)prop-2-enamide(Non-covalent)

YR6.6: 15 residues within 4Å: Chain A: T.51, D.67, V.68, M.69, G.144, P.146, D.159, T.161, V.200, K.202, R.216, S.218, S.220 Ligands: ATP.4, EDO.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.159, A:T.161 Hydrogen bonds: A:R.216, A:R.216, A:S.218, A:S.220 Water bridges: A:D.67, A:S.145

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 2 residues within 4Å: Chain A: Y.54, H.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.57 Water bridges: A:Y.54, A:H.57, A:H.57 EDO.8: 7 residues within 4Å: Chain A: Y.88, K.202, R.216, F.328, L.330 Ligands: ATP.4, YR6.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.88, A:K.202, A:R.216 EDO.9: 3 residues within 4Å: Chain A: K.224, E.225, N.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.228 Water bridges: A:K.224, A:E.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Groebke-Zbinden, K. et al., Crystal Structure of a human cyclic GMP-AMP synthase complex. To be published

Release Date

2024-02-21

Peptides

Cyclic GMP-AMP synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclic GMP-AMP synthase

Related Entries With Identical Sequence