SMTL ID : 4d3j.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 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, F.235, N.236, G.237, W.238, M.240, E.243, R.247, V.300, W.329, Y.355, Y.357 Ligands: XFN.3 17 PLIP interactions: 17 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:W.238, A:E.243, A:V.300, A:W.329, A:Y.355 Hydrogen bonds: A:R.247 Water bridges: A:R.65 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.10: 17 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, F.235, N.236, G.237, W.238, M.240, E.243, R.247, V.300, W.329, Y.355, Y.357 Ligands: XFN.12 17 PLIP interactions: 17 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:W.238, B:E.243, B:V.300, B:W.329, B:Y.355 Hydrogen bonds: B:R.247 Water bridges: B:R.65 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: 5 residues within 4Å: Chain A: Q.129, Y.239, R.247, N.248 Ligands: XFN.3 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: Q.129, Y.239, R.247, N.248 Ligands: XFN.12 Ligand excluded by PLIP

2 x XFN: 6,6'-[(5-aminobenzene-1,3-diyl)diethane-2,1-diyl]bis(4-methylpyridin-2-amine)(Non-covalent)

XFN.3: 18 residues within 4Å: Chain A: H.128, Q.129, R.132, P.216, I.218, F.235, G.237, W.238, Y.239, E.243, R.247, T.328, W.329 Chain B: F.342 Ligands: HEM.1, CL.2, POL.9, GOL.15 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.218, A:F.235, A:W.329 Hydrogen bonds: A:H.128, A:E.243, A:T.328 Water bridges: A:R.132 pi-Stacking: A:W.329 pi-Cation interactions: A:R.247 XFN.12: 18 residues within 4Å: Chain A: F.342 Chain B: H.128, Q.129, R.132, P.216, I.218, F.235, G.237, W.238, Y.239, E.243, R.247, T.328, W.329 Ligands: GOL.6, HEM.10, CL.11, POL.18 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.218, B:F.235, B:W.329 Hydrogen bonds: B:H.128, B:E.243, B:T.328 Water bridges: B:R.132 pi-Stacking: B:W.329 pi-Cation interactions: B:R.247

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: E.156, W.160, R.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.160 GOL.5: 2 residues within 4Å: Chain A: 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 GOL.6: 5 residues within 4Å: Chain A: W.327, F.342, R.344 Chain B: T.328 Ligands: XFN.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.328, B:T.328 GOL.7: 7 residues within 4Å: Chain A: R.142, I.143, G.144, D.166, R.254, Y.255, K.257 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.144, A:D.166, A:K.257, A:K.257 Water bridges: A:R.142, A:D.166, A:R.254 GOL.13: 3 residues within 4Å: Chain B: E.156, W.160, R.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.160 GOL.14: 2 residues within 4Å: Chain B: 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 GOL.15: 5 residues within 4Å: Chain A: T.328 Chain B: W.327, F.342, R.344 Ligands: XFN.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.328, A:T.328 GOL.16: 7 residues within 4Å: Chain B: R.142, I.143, G.144, D.166, R.254, Y.255, K.257 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.144, B:D.166, B:K.257, B:K.257 Water bridges: B:R.142, B:D.166, B:R.254

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

PEG.8: 7 residues within 4Å: Chain A: A.337, A.338, H.343 Chain B: A.250, D.251, E.252, L.258 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.252, A:T.339 Water bridges: B:A.246, B:E.252 PEG.17: 7 residues within 4Å: Chain A: A.250, D.251, E.252, L.258 Chain B: A.337, A.338, H.343 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.252, B:T.339 Water bridges: A:A.246, A:E.252

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

POL.9: 4 residues within 4Å: Chain A: H.128, R.132, A.147 Ligands: XFN.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.132, A:R.132 POL.18: 4 residues within 4Å: Chain B: H.128, R.132, A.147 Ligands: XFN.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.132, B:R.132

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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