SMTL ID : 7d9s.1

Structure of huamn soluble guanylate cyclase in the YC1 and NO-bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.486, I.487, D.530 Ligands: MG.2, G2P.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.486, A:D.530 MG.2: 6 residues within 4Å: Chain A: D.486, I.487, V.488, D.530 Ligands: MG.1, G2P.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.486, A:D.486, A:I.487

1 x YC1: [5-[1-(phenylmethyl)indazol-3-yl]furan-2-yl]methanol(Non-covalent)

YC1.3: 14 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, E.370 Ligands: HEM.4 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:L.425, B:Y.2, B:F.4, B:F.4, B:F.77, B:Y.83, B:Y.83 Hydrogen bonds: B:E.370 pi-Stacking: B:F.4, B:Y.112

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

HEM.4: 20 residues within 4Å: Chain B: M.1, Y.2, F.74, L.87, L.101, L.104, H.105, L.108, M.115, R.116, F.120, Y.135, S.137, R.139, L.142, I.145, V.146, I.149, I.150 Ligands: YC1.3 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:Y.2, B:F.74, B:L.101, B:L.101, B:L.104, B:L.108, B:F.120, B:Y.135, B:L.142, B:I.145, B:I.145, B:V.146, B:I.149, B:I.150 Hydrogen bonds: B:M.1, B:Y.2, B:R.116, B:R.116, B:R.116, B:S.137 Salt bridges: B:R.139, B:R.139 pi-Stacking: B:H.105

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

G2P.5: 22 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, M.480, L.542, V.547, N.548, S.551, R.552, K.593 Ligands: MG.1, MG.2 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.489, A:F.490, B:S.551, B:R.552, B:R.552 Salt bridges: A:R.574, B:E.473, B:K.593

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, R. et al., Activation mechanism of human soluble guanylate cyclase by stimulators and activators. Nat Commun (2021)

Release Date

2021-08-11

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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