SMTL ID : 4ugi.1

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with N1-(6-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)pyridin-2-yl)-N1,N2- dimethylethane-1,2-diamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 15 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, L.75, F.235, N.236, G.237, W.238, M.240, E.243, Y.355, Y.357 Ligands: SKO.3, GOL.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:R.65, A:L.75, A:F.235, A:F.235, A:W.238, A:E.243, A:Y.355, A:Y.355 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.11: 15 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, L.75, F.235, N.236, G.237, W.238, M.240, E.243, Y.355, Y.357 Ligands: SKO.13, GOL.15 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:R.65, B:L.75, B:F.235, B:F.235, B:W.238, B:E.243, B:Y.355, B:Y.355 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

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

CL.2: 3 residues within 4Å: Chain A: Q.129, Y.239, N.248 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: Q.129, Y.239, N.248 Ligand excluded by PLIP

2 x SKO: N'-[6-[2-(6-AZANYL-4-METHYL-PYRIDIN-2-YL)ETHYL]PYRIDIN-2-YL]-N,N'-DIMETHYL-ETHANE-1,2-DIAMINE(Non-covalent)

SKO.3: 15 residues within 4Å: Chain A: H.128, Q.129, P.216, I.218, M.221, F.235, N.236, G.237, W.238, Y.239, M.240, E.243, W.329, Y.357 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.216, A:I.218, A:I.218, A:F.235 Hydrogen bonds: A:M.240, A:E.243, A:Y.357 SKO.13: 15 residues within 4Å: Chain B: H.128, Q.129, P.216, I.218, M.221, F.235, N.236, G.237, W.238, Y.239, M.240, E.243, W.329, Y.357 Ligands: HEM.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.216, B:I.218, B:I.218, B:F.235 Hydrogen bonds: B:M.240, B:E.243, B:Y.357

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 5 residues within 4Å: Chain A: T.328, W.329 Chain B: W.327, F.342 Ligands: POL.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.247 pi-Stacking: A:W.329 IMD.14: 5 residues within 4Å: Chain A: W.327, F.342 Chain B: T.328, W.329 Ligands: POL.19 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.247 pi-Stacking: B:W.329

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: M.221, Y.355, F.356, Y.357 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.357 GOL.6: 3 residues within 4Å: Chain A: W.238, S.298, I.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.238, A:S.298, A:I.299 GOL.7: 3 residues within 4Å: Chain A: V.183, W.184, Y.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.184 Water bridges: A:L.158, A:P.182 GOL.15: 5 residues within 4Å: Chain B: M.221, Y.355, F.356, Y.357 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.357 GOL.16: 3 residues within 4Å: Chain B: W.238, S.298, I.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.238, B:S.298, B:I.299 GOL.17: 3 residues within 4Å: Chain B: V.183, W.184, Y.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.184 Water bridges: B:L.158, B:P.182

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

POL.8: 5 residues within 4Å: Chain A: G.144, D.166, R.254, Y.255, K.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.166, A:K.257 Water bridges: A:G.144, A:D.166 POL.9: 5 residues within 4Å: Chain A: T.328 Chain B: W.327, R.344, S.345 Ligands: IMD.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.327, A:T.328 Hydrogen bonds: B:W.327 POL.10: 4 residues within 4Å: Chain A: K.49, D.79, R.81, D.82 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.81 Hydrogen bonds: A:K.49, A:K.49, A:R.81 Water bridges: A:D.82 POL.18: 5 residues within 4Å: Chain B: G.144, D.166, R.254, Y.255, K.257 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.166, B:K.257 Water bridges: B:G.144, B:D.166 POL.19: 5 residues within 4Å: Chain A: W.327, R.344, S.345 Chain B: T.328 Ligands: IMD.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.328, A:W.327 Hydrogen bonds: A:W.327 POL.20: 4 residues within 4Å: Chain B: K.49, D.79, R.81, D.82 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.81 Hydrogen bonds: B:K.49, B:K.49, B:R.81 Water bridges: B:D.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Inhibitor Bound Crystal Structures of Bacterial Nitric Oxide Synthase. Biochemistry (2015)

Release Date

2015-06-24

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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