SMTL ID : 7utt.1

Structure of Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP synthase (cGAS) through Mn coordination

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.1: 15 residues within 4Å: Chain A: G.55, S.56, K.62, E.68, D.70, R.221, S.225, E.228, K.259, S.277, Y.278, K.281, H.324 Ligands: MN.3, MN.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.56, A:S.56, A:S.225, A:S.277, A:K.281, A:K.281 Water bridges: A:G.55, A:G.55, A:Y.57, A:E.59, A:E.68, A:E.68, A:R.221, A:K.259, A:K.259, A:K.259, A:Y.278, A:K.281 Salt bridges: A:K.259 pi-Stacking: A:Y.278, A:Y.278 pi-Cation interactions: A:R.221 APC.5: 15 residues within 4Å: Chain B: G.55, S.56, K.62, E.68, D.70, R.221, S.225, E.228, K.259, S.277, Y.278, K.281, H.324 Ligands: MN.7, MN.8 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:S.56, B:S.56, B:S.225, B:S.277, B:K.281, B:K.281 Water bridges: B:G.55, B:Y.57, B:E.59, B:R.221, B:R.221, B:R.221, B:R.221, B:K.259, B:K.259, B:S.277, B:Y.278, B:Y.278, B:K.281 Salt bridges: B:K.259 pi-Stacking: B:Y.278, B:Y.278 pi-Cation interactions: B:R.221

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: APC.1, MN.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.68, A:D.70, A:D.164, H2O.2, H2O.3 MN.4: 5 residues within 4Å: Chain A: S.56, E.68, D.70 Ligands: APC.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: APC.5, MN.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.68, B:D.70, B:D.164, H2O.7, H2O.8 MN.8: 5 residues within 4Å: Chain B: S.56, E.68, D.70 Ligands: APC.5, MN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.68, B:D.70, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, S. et al., Structure of Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP synthase (cGAS) through Mn coordination. To Be Published

Release Date

2023-05-03

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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