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

Structure of Bacillus subtilis nitric oxide synthase in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 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, P.108, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: QJ8.2, H4B.3 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:R.65, A:P.108, A:F.235, A:F.235, A:W.238, A:E.243, A:V.300, A:W.329, A:Y.355, A:Y.355 Hydrogen bonds: A:Y.357 Water bridges: A:R.247 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, P.108, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: QJ8.9, H4B.10 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:R.65, B:P.108, B:F.235, B:F.235, B:W.238, B:E.243, B:V.300, B:W.329, B:Y.355, B:Y.355 Hydrogen bonds: B:Y.357 Water bridges: B:R.247 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

2 x QJ8: 6-({[(3R,5S)-5-{[(6-amino-4-methylpyridin-2-yl)methoxy]methyl}pyrrolidin-3-yl]oxy}methyl)-4-methylpyridin-2-amine(Non-covalent)

QJ8.2: 12 residues within 4Å: Chain A: H.128, P.216, I.218, D.220, F.235, G.237, W.238, Y.239, E.243, W.329, Y.357 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.218, A:F.235 Hydrogen bonds: A:D.220, A:M.240, A:E.243, A:Y.357 pi-Stacking: A:Y.357 QJ8.9: 12 residues within 4Å: Chain B: H.128, P.216, I.218, D.220, F.235, G.237, W.238, Y.239, E.243, W.329, Y.357 Ligands: HEM.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.218, B:F.235 Hydrogen bonds: B:D.220, B:M.240, B:E.243, B:Y.357 pi-Stacking: B:Y.357

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

H4B.3: 8 residues within 4Å: Chain A: R.247, T.328, W.329 Chain B: W.327, F.342, H.343, R.344 Ligands: HEM.1 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.247, A:T.328, A:W.329, B:W.327 pi-Stacking: A:W.329, A:W.329 pi-Cation interactions: A:W.329, A:W.329 H4B.10: 8 residues within 4Å: Chain A: W.327, F.342, H.343, R.344 Chain B: R.247, T.328, W.329 Ligands: HEM.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.247, B:T.328, B:W.329, A:W.327 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.4: 4 residues within 4Å: Chain A: Q.129, Y.213, Y.239, N.248 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: Q.129, Y.213, Y.239, N.248 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.6: 8 residues within 4Å: Chain A: R.142, I.143, G.144, P.146, D.166, R.254, Y.255, K.257 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.142, A:G.144, A:R.254, A:K.257 Water bridges: A:K.257, A:K.257 GOL.7: 2 residues within 4Å: Chain A: V.183, W.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.184, A:W.184 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: 8 residues within 4Å: Chain B: R.142, I.143, G.144, P.146, D.166, R.254, Y.255, K.257 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.142, B:G.144, B:R.254, B:K.257 Water bridges: B:K.257, B:K.257 GOL.14: 2 residues within 4Å: Chain B: V.183, W.184 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.184, B:W.184

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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