SMTL ID : 4ugq.1

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with N,N''-(((2S)-3-aminopropane-1,2-diyl)bis(oxymethanediylbenzene-3,1- diyl))dithiophene-2-carboximidamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, L.75, P.108, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: H4B.2, 7LN.4, GOL.5 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:I.67, A:L.75, A:P.108, A:F.235, 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 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.7: 20 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, L.75, P.108, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: H4B.8, 7LN.10, GOL.11 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:I.67, B:L.75, B:P.108, B:F.235, 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 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 Ligands: HEM.1, 7LN.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.247, A:T.328, A:W.329 Water bridges: A:R.247, A:R.247 pi-Stacking: A:W.329, A:W.329 pi-Cation interactions: A:W.329 H4B.8: 9 residues within 4Å: Chain A: W.327, F.342, H.343, R.344 Chain B: R.247, T.328, W.329 Ligands: HEM.7, 7LN.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.247, B:T.328, B:W.329 Water bridges: B:R.247, B:R.247 pi-Stacking: B:W.329, B:W.329 pi-Cation interactions: B:W.329

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.9: 3 residues within 4Å: Chain B: Q.129, Y.239, N.248 Ligand excluded by PLIP

2 x 7LN: N,N''-{[(2S)-3-aminopropane-1,2-diyl]bis(oxymethanediylbenzene-3,1-diyl)}dithiophene-2-carboximidamide(Non-covalent)

7LN.4: 15 residues within 4Å: Chain A: H.128, Q.129, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, E.243, Y.357, Q.358, D.359 Ligands: HEM.1, H4B.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.216, A:I.218, A:I.218, A:F.235, A:Y.357, A:Y.357 Hydrogen bonds: A:E.243 7LN.10: 15 residues within 4Å: Chain B: H.128, Q.129, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, E.243, Y.357, Q.358, D.359 Ligands: HEM.7, H4B.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.216, B:I.218, B:I.218, B:F.235, B:Y.357, B:Y.357 Hydrogen bonds: B:E.243

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.355, A:Y.357 GOL.6: 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:S.298, A:I.299 GOL.11: 6 residues within 4Å: Chain B: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEM.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.355, B:Y.357 GOL.12: 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:S.298, B:I.299

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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