SMTL ID : 4ugw.1

Structure of Y357F Bacillus subtilis Nitric Oxide Synthase in complex with 6-(5-((3R,4R)-4-((6-azanyl-4-methyl-pyridin-2-yl)methyl) pyrrolidin-3-yl)oxypentyl)-4-methyl-pyridin-2-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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, L.75, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355 Ligands: H4B.2, HW1.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:R.65, A:I.67, A:F.235, A:F.235, A:F.235, A:W.238, A:W.238, A:E.243, A:V.300, A:Y.355, A:Y.355 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: 18 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 Ligands: H4B.7, HW1.9 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:R.65, B:I.67, B:F.235, B:F.235, B:F.235, B:W.238, B:W.238, B:E.243, B:V.300, B:Y.355, B:Y.355 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 H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.2: 8 residues within 4Å: Chain A: R.247, T.328, W.329 Chain B: W.327, F.342, H.343 Ligands: HEM.1, HW1.4 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:W.327 Hydrogen bonds: A:R.247, A:T.328, A:W.329 pi-Stacking: A:W.329, A:W.329 H4B.7: 8 residues within 4Å: Chain A: W.327, F.342, H.343 Chain B: R.247, T.328, W.329 Ligands: HEM.6, HW1.9 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.247, B:T.328, B:W.329 pi-Stacking: B:W.329, B:W.329 Water bridges: A:W.327

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

CL.3: 3 residues within 4Å: Chain A: Q.129, Y.239, N.248 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: Q.129, Y.239, N.248 Ligand excluded by PLIP

2 x HW1: 6-[5-({(3R,4R)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}oxy)pentyl]-4-methylpyridin-2-amine(Non-covalent)

HW1.4: 16 residues within 4Å: Chain A: R.65, H.128, Q.129, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, M.240, E.243, W.329, F.357 Ligands: HEM.1, H4B.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.216, A:I.218, A:F.235, A:F.357, A:F.357 Hydrogen bonds: A:R.65, A:M.240, A:E.243 Water bridges: A:R.65, A:F.357 HW1.9: 16 residues within 4Å: Chain B: R.65, H.128, Q.129, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, M.240, E.243, W.329, F.357 Ligands: HEM.6, H4B.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.216, B:I.218, B:F.235, B:F.357, B:F.357 Hydrogen bonds: B:R.65, B:M.240, B:E.243 Water bridges: B:R.65, B:F.357

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: W.238, S.298, I.299, V.300, Q.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.298, A:I.299, A:Q.308 GOL.10: 5 residues within 4Å: Chain B: W.238, S.298, I.299, V.300, Q.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.298, B:I.299, B:Q.308

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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