SMTL ID : 8hbf.1

Structure of human soluble guanylate cyclase in the NO+Rio state at 3.1 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.1: 21 residues within 4Å: Chain A: D.486, I.487, V.488, G.489, F.490, T.491, I.528, G.529, D.530, R.574 Chain B: F.424, E.473, V.475, L.542, V.547, N.548, S.551, R.552, K.593 Ligands: MG.2, MG.3 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.548, B:S.551, B:R.552, B:R.552, B:K.593, B:K.593, B:K.593, A:G.489, A:F.490, A:T.491 Salt bridges: B:E.473, B:K.593, A:R.574

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.486, D.530 Ligands: G2P.1, MG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.486, A:D.530 MG.3: 5 residues within 4Å: Chain A: D.486, I.487, D.530 Ligands: G2P.1, MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.486, A:D.486, A:I.487, A:D.530

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.4: 23 residues within 4Å: Chain B: M.1, Y.2, F.4, V.5, F.74, L.87, F.97, L.101, L.104, H.105, L.108, M.115, R.116, F.120, Y.135, S.137, R.139, I.145, V.146, I.149, I.150 Ligands: GZO.5, NO.6 28 PLIP interactions: 27 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.4, B:F.4, B:V.5, B:F.74, B:F.74, B:L.87, B:F.97, B:L.101, B:L.101, B:L.104, B:L.108, B:L.108, B:F.120, B:Y.135, B:I.145, B:I.149, B:I.149, B:I.150 Hydrogen bonds: B:Y.2, B:R.116, B:R.116, B:R.116, B:Y.135, B:S.137 Salt bridges: B:R.139, B:R.139 pi-Stacking: B:H.105 Metal complexes: NO.6

1 x GZO: methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-carbamate(Non-covalent)

GZO.5: 15 residues within 4Å: Chain A: L.425, R.428, L.429 Chain B: Y.2, F.4, V.39, R.40, F.77, C.78, S.81, Y.83, Y.112, Y.363, E.370 Ligands: HEM.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.2, B:F.4, B:F.4, B:F.77, B:F.77 Hydrogen bonds: B:R.40, B:S.81, B:E.370 pi-Stacking: B:F.4, B:Y.83, B:Y.83, B:Y.112

1 x NO: NITRIC OXIDE(Non-covalent)

NO.6: 4 residues within 4Å: Chain B: F.4, F.74, I.149 Ligands: HEM.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, R. et al., NO binds to the distal site of haem in the fully activated soluble guanylate cyclase. Nitric Oxide (2023)

Release Date

2023-04-19

Peptides

Guanylate cyclase soluble subunit alpha-1: A
Guanylate cyclase soluble subunit beta-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Guanylate cyclase soluble subunit alpha-1

Guanylate cyclase soluble subunit beta-1

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