SMTL ID : 5g6q.1

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 7-(((5-((Methylamino)methyl)pyridin-3-yl)oxy)methyl) quinolin-2-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: H4B.2, TUE.4, BTB.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:R.65, A:I.67, A:F.235, A:W.238, A:W.238, A:E.243, A:V.300, A:Y.355 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.8: 19 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: H4B.9, TUE.11, BTB.12 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:R.65, B:I.67, B:F.235, B:W.238, B:W.238, B:E.243, B:V.300, B:Y.355 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.2: 9 residues within 4Å: Chain A: R.247, T.328, W.329 Chain B: W.327, F.342, H.343, R.344, S.345 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.247, A:R.247, A:T.328, A:W.329 pi-Stacking: A:W.329, A:W.329 pi-Cation interactions: A:W.329, A:W.329 H4B.9: 9 residues within 4Å: Chain A: W.327, F.342, H.343, R.344, S.345 Chain B: R.247, T.328, W.329 Ligands: HEM.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.247, B:R.247, B:T.328, B:W.329 pi-Stacking: B:W.329, B:W.329 pi-Cation interactions: B:W.329, B:W.329

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

CL.3: 4 residues within 4Å: Chain A: Q.129, Y.213, Y.239, N.248 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: Q.129, Y.213, Y.239, N.248 Ligand excluded by PLIP

2 x TUE: 7-[[5-[(methylideneamino)methyl]pyridin-3-yl]oxymethyl]quinolin-2-amine(Non-covalent)

TUE.4: 12 residues within 4Å: Chain A: H.128, P.216, I.218, M.221, F.235, G.237, W.238, Y.239, M.240, E.243, Y.357 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.218, A:F.235 Hydrogen bonds: A:W.238, A:M.240 Water bridges: A:R.132 pi-Stacking: A:H.128 TUE.11: 12 residues within 4Å: Chain B: H.128, P.216, I.218, M.221, F.235, G.237, W.238, Y.239, M.240, E.243, Y.357 Ligands: HEM.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.218, B:F.235 Hydrogen bonds: B:W.238, B:M.240 Water bridges: B:R.132 pi-Stacking: B:H.128

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.5: 8 residues within 4Å: Chain A: R.65, M.221, I.350, N.354, Y.355, F.356, Y.357 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.354, A:N.354, A:Y.357 Water bridges: A:R.65, A:R.65, A:D.326, A:Y.355 BTB.12: 8 residues within 4Å: Chain B: R.65, M.221, I.350, N.354, Y.355, F.356, Y.357 Ligands: HEM.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.354, B:N.354, B:Y.357 Water bridges: B:R.65, B:R.65, B:D.326, B:Y.355

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: W.238, S.298, I.299, Q.308 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.298, A:I.299, A:Q.308 Water bridges: A:W.238, A:Q.308 GOL.7: 6 residues within 4Å: Chain A: R.142, G.144, D.166, R.254, Y.255, K.257 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.142, A:R.254, A:K.257, A:K.257 Water bridges: A:D.166 GOL.13: 4 residues within 4Å: Chain B: W.238, S.298, I.299, Q.308 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.298, B:I.299, B:Q.308 Water bridges: B:W.238, B:Q.308 GOL.14: 6 residues within 4Å: Chain B: R.142, G.144, D.166, R.254, Y.255, K.257 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.142, B:R.254, B:K.257, B:K.257 Water bridges: B:D.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Targeting Bacterial Nitric Oxide Synthase with Aminoquinoline-Based Inhibitors. Biochemistry (2016)

Release Date

2016-09-21

Peptides

NITRIC OXIDE SYNTHASE OXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NITRIC OXIDE SYNTHASE OXYGENASE

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