SMTL ID : 4d7j.1

Structure of Bacillus subtilis nitric oxide synthase in complex with 6-(4-(((3-Fluorophenethyl)amino)methyl)phenyl)-4-methylpyridin-2- amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, L.75, 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, 0GD.4, PEG.8, GOL.10 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:I.67, A:L.75, A:F.235, A:F.235, A:W.238, A:W.238, A:E.243, A:V.300, A:Y.355, A:Y.355 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.11: 21 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, L.75, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: H4B.12, 0GD.14, PEG.18, GOL.20 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:I.67, B:L.75, B:F.235, B:F.235, B:W.238, B:W.238, B:E.243, B:V.300, B:Y.355, 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 7 PLIP interactions: 7 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 H4B.12: 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.11 7 PLIP interactions: 7 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

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

CL.3: 4 residues within 4Å: Chain A: Q.129, R.132, Y.239, N.248 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: Q.129, R.132, Y.239, N.248 Ligand excluded by PLIP

2 x 0GD: 6-[4-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]-4-methylpyridin-2-amine(Non-covalent)

0GD.4: 14 residues within 4Å: Chain A: H.128, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, M.240, E.243, W.329, Y.357 Ligands: HEM.1, PEG.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.218, A:F.235 Hydrogen bonds: A:M.240, A:E.243 0GD.14: 14 residues within 4Å: Chain B: H.128, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, M.240, E.243, W.329, Y.357 Ligands: HEM.11, PEG.18 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.218, B:F.235 Hydrogen bonds: B:M.240, B:E.243

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: W.238, S.298, I.299, V.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.238, A:I.299 Water bridges: A:V.297 GOL.6: 7 residues within 4Å: Chain A: R.142, I.143, G.144, D.166, R.254, Y.255, K.257 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.142, A:R.142, A:G.144, A:D.166, A:K.257 Water bridges: A:R.142, A:D.166, A:R.254 GOL.7: 3 residues within 4Å: Chain A: V.183, W.184, Y.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.184, A:W.184 GOL.10: 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:Y.355, A:Y.357 Water bridges: A:Y.355 GOL.15: 4 residues within 4Å: Chain B: W.238, S.298, I.299, V.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.238, B:I.299 Water bridges: B:V.297 GOL.16: 7 residues within 4Å: Chain B: R.142, I.143, G.144, D.166, R.254, Y.255, K.257 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.142, B:R.142, B:G.144, B:D.166, B:K.257 Water bridges: B:R.142, B:D.166, B:R.254 GOL.17: 3 residues within 4Å: Chain B: V.183, W.184, Y.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.184, B:W.184 GOL.20: 6 residues within 4Å: Chain B: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEM.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.355, B:Y.357 Water bridges: B:Y.355

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain A: H.128, I.218, D.220, M.221, Y.357 Ligands: HEM.1, 0GD.4 No protein-ligand interaction detected (PLIP) PEG.18: 7 residues within 4Å: Chain B: H.128, I.218, D.220, M.221, Y.357 Ligands: HEM.11, 0GD.14 No protein-ligand interaction detected (PLIP)

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

POL.9: 4 residues within 4Å: Chain A: S.263, G.266, I.267, A.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.263 POL.19: 4 residues within 4Å: Chain B: S.263, G.266, I.267, A.268 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Nitric Oxide Synthase as a Target for Methicillin-Resistant Staphylococcus Aureus. Chem.Biol. (2015)

Release Date

2015-07-01

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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