SMTL ID : 4d3i.1

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6,6'-((5-(aminomethyl)-1,3-phenylene)bis(ethane-2,1-diyl))bis(4- methylpyridin-2-amine)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, P.108, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: 1ET.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:R.65, A:I.67, A:P.108, A:F.235, A:F.235, A:W.238, A:W.238, A:E.243, A:V.300, A:W.329, A:Y.355 Hydrogen bonds: A:W.329 Water bridges: A:R.65, A:R.247 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.6: 17 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, P.108, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: 1ET.7 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:R.65, B:I.67, B:P.108, B:F.235, B:F.235, B:W.238, B:W.238, B:E.243, B:V.300, B:W.329, B:Y.355 Hydrogen bonds: B:W.329 Water bridges: B:R.65, B:R.247 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

2 x 1ET: 6,6'-{[5-(aminomethyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine)(Non-covalent)

1ET.2: 15 residues within 4Å: Chain A: H.128, P.216, I.218, F.235, G.237, W.238, Y.239, E.243, R.247, T.328, W.329, Y.357 Chain B: F.342 Ligands: HEM.1, POL.5 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.218, A:F.235, A:W.329, B:F.342 Hydrogen bonds: A:E.243, A:R.247, A:T.328, A:Y.357 pi-Stacking: A:W.329 pi-Cation interactions: A:R.247 1ET.7: 15 residues within 4Å: Chain A: F.342 Chain B: H.128, P.216, I.218, F.235, G.237, W.238, Y.239, E.243, R.247, T.328, W.329, Y.357 Ligands: HEM.6, POL.10 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.218, B:F.235, B:W.329, A:F.342 Hydrogen bonds: B:E.243, B:R.247, B:T.328, B:Y.357 pi-Stacking: B:W.329 pi-Cation interactions: B:R.247

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.156, W.160, R.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.160 Water bridges: A:R.161 GOL.8: 3 residues within 4Å: Chain B: E.156, W.160, R.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.160 Water bridges: B:R.161

4 x POL: N-PROPANOL(Non-covalent)

POL.4: 3 residues within 4Å: Chain A: D.270, Y.271, N.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.272, A:N.272 Water bridges: A:T.273 POL.5: 4 residues within 4Å: Chain A: E.243, R.247, N.248 Ligands: 1ET.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.247 Hydrogen bonds: A:E.243 Water bridges: A:N.248, A:R.254 POL.9: 3 residues within 4Å: Chain B: D.270, Y.271, N.272 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.272, B:N.272 Water bridges: B:T.273 POL.10: 4 residues within 4Å: Chain B: E.243, R.247, N.248 Ligands: 1ET.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.247 Hydrogen bonds: B:E.243 Water bridges: B:N.248, B:R.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors. J.Med.Chem. (2015)

Release Date

2015-01-14

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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