SMTL ID : 7fun.1

Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-[(4-benzylpiperazin-1-yl)methyl]-6-(2-chloro-4-methylphenyl)-1H-benzimidazole-4-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 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

1 x YU6: (5M)-2-[(4-benzylpiperazin-1-yl)methyl]-5-(2-chloro-4-methylphenyl)-1H-benzimidazole-7-carboxylic acid(Non-covalent)

YU6.2: 22 residues within 4Å: Chain A: L.49, E.56, D.67, V.68, M.69, T.161, R.216, S.218, F.219, S.220, I.222, E.223, I.226, Y.276, K.279, T.280, F.283, Y.323, F.324 Ligands: IOD.4, IOD.5, CL.10 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.49, A:E.56, A:M.69, A:E.223, A:I.226, A:Y.276, A:F.283, A:F.283, A:Y.323 Hydrogen bonds: A:F.219 Water bridges: A:R.216, A:R.216, A:N.322 Salt bridges: A:D.67, A:D.67, A:R.216 pi-Stacking: A:F.324 Halogen bonds: A:T.280

7 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain A: L.227, K.251 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: L.48, N.50, M.69 Ligands: YU6.2 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: R.216, S.218 Ligands: YU6.2 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: E.258, K.261, S.275 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: K.232 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: A.186, R.189, K.190 Ligand excluded by PLIP IOD.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 5 residues within 4Å: Chain A: V.58, S.274, S.275, Y.276 Ligands: YU6.2 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.16, I.60 Ligand excluded by PLIP

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

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