SMTL ID : 4lwa.2 (1 other biounit)

Structure of Bacillus subtilis nitric oxide synthase in complex with ((2S, 3S)-1,3-bis((6-(2,5-dimethyl-1H-pyrrol-1-yl)-4-methylpyridin-2-yl)methoxy)-2-aminobutane

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 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: Q13.2, GOL.6 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:R.65, A:F.235, A:F.235, A:W.238, A:M.240, A:V.300, A:W.329, A:Y.355, A:Y.355 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.9: 18 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: Q13.10, GOL.14 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:R.65, B:F.235, B:F.235, B:W.238, B:M.240, B:V.300, B:W.329, B:Y.355, B:Y.355 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

2 x Q13: 6,6'-{[(2S,3S)-2-aminobutane-1,3-diyl]bis(oxymethanediyl)}bis(4-methylpyridin-2-amine)(Non-covalent)

Q13.2: 11 residues within 4Å: Chain A: I.218, F.235, N.236, G.237, W.238, Y.239, E.243, R.247, W.329 Ligands: HEM.1, CL.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.218, A:I.218, A:F.235 Hydrogen bonds: A:M.240, A:E.243, A:E.243, A:R.247, A:W.329 pi-Stacking: A:W.329 pi-Cation interactions: A:R.247 Q13.10: 11 residues within 4Å: Chain B: I.218, F.235, N.236, G.237, W.238, Y.239, E.243, R.247, W.329 Ligands: HEM.9, CL.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.218, B:I.218, B:F.235 Hydrogen bonds: B:M.240, B:E.243, B:E.243, B:R.247, B:W.329 pi-Stacking: B:W.329 pi-Cation interactions: B:R.247

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

CL.3: 4 residues within 4Å: Chain A: Q.129, Y.239, N.248 Ligands: Q13.2 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: Q.129, Y.239, N.248 Ligands: Q13.10 Ligand excluded by PLIP

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.238, S.298, I.299, V.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.238, A:I.299 GOL.5: 3 residues within 4Å: Chain A: D.270, Y.271, N.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.272, A:N.272 GOL.6: 6 residues within 4Å: Chain A: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.65, A:Y.357 Water bridges: A:N.354 GOL.7: 5 residues within 4Å: Chain A: W.327, F.342, R.344, S.345 Chain B: T.328 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.342, B:T.328, B:T.328 GOL.8: 7 residues within 4Å: Chain A: R.142, G.144, P.146, D.166, R.254, Y.255, K.257 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.142, A:D.166, A:K.257, A:K.257 Water bridges: A:R.142, A:D.166, A:R.254 GOL.12: 4 residues within 4Å: Chain B: W.238, S.298, I.299, V.300 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.238, B:I.299 GOL.13: 3 residues within 4Å: Chain B: D.270, Y.271, N.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.272, B:N.272 GOL.14: 6 residues within 4Å: Chain B: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEM.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.65, B:Y.357 Water bridges: B:N.354 GOL.15: 5 residues within 4Å: Chain A: T.328 Chain B: W.327, F.342, R.344, S.345 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.342, A:T.328, A:T.328 GOL.16: 7 residues within 4Å: Chain B: R.142, G.144, P.146, D.166, R.254, Y.255, K.257 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.142, B:D.166, B:K.257, B:K.257 Water bridges: B:R.142, B:D.166, B:R.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Structural and biological studies on bacterial nitric oxide synthase inhibitors. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-10-23

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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