SMTL ID : 3n5r.1

Structure of endothelial nitric oxide synthase heme domain complexed with 4-(3-(2-(6-amino-4-methylpyridin-2-yl)ethyl)phenethyl)-6-methylpyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: W.142, A.145, R.147, C.148, V.149, G.150, S.190, F.317, S.318, G.319, W.320, M.322, E.325, W.411, F.437, Y.439 Ligands: H4B.6, XFH.7 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.142, A:W.142, A:W.142, A:A.145, A:R.147, A:V.149, A:F.317, A:F.317, A:W.320, A:E.325, A:W.411, A:W.411, A:F.437, A:F.437, A:F.437 Hydrogen bonds: A:Y.439 Water bridges: A:E.325 Salt bridges: A:R.147 pi-Stacking: A:W.142 Metal complexes: A:C.148 HEM.9: 19 residues within 4Å: Chain B: W.142, A.145, R.147, C.148, V.149, G.150, S.190, F.317, S.318, G.319, W.320, M.322, E.325, W.411, F.437, Y.439 Ligands: ACT.10, H4B.13, XFH.14 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.142, B:W.142, B:W.142, B:A.145, B:R.147, B:V.149, B:F.317, B:F.317, B:W.320, B:W.411, B:F.437, B:F.437 Salt bridges: B:R.147 pi-Stacking: B:W.142 Metal complexes: B:C.148

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: Q.211, R.214, N.330, R.336 Ligands: XFH.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.211, A:N.330, A:N.330 Salt bridges: A:R.214, A:R.336 ACT.3: 5 residues within 4Å: Chain A: G.150, I.152, W.320, V.382, S.390 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.152 Hydrogen bonds: A:W.320, A:S.390 ACT.10: 6 residues within 4Å: Chain B: G.150, I.152, W.320, V.382, S.390 Ligands: HEM.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.390, B:S.390

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: V.68, R.329, H.335 Chain B: W.38 Ligands: H4B.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.329, A:R.329, A:H.335 GOL.11: 7 residues within 4Å: Chain A: W.38 Chain B: V.68, R.329, H.335, W.411 Ligands: H4B.13, XFH.14 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.329, B:R.329, B:H.335, A:H.425

2 x CAD: CACODYLIC ACID(Non-covalent)

CAD.5: 2 residues within 4Å: Chain A: W.286, C.346 No protein-ligand interaction detected (PLIP) CAD.12: 2 residues within 4Å: Chain B: W.286, C.346 No protein-ligand interaction detected (PLIP)

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.6: 12 residues within 4Å: Chain A: S.66, V.68, R.329, A.410, W.411 Chain B: W.409, F.424, H.425, Q.426, E.427 Ligands: HEM.1, GOL.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.329, A:A.410, A:W.411 pi-Stacking: A:W.411, A:W.411 pi-Cation interactions: A:W.411 Hydrophobic interactions: B:E.427 H4B.13: 11 residues within 4Å: Chain A: W.409, F.424, H.425, E.427 Chain B: S.66, V.68, R.329, A.410, W.411 Ligands: HEM.9, GOL.11 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.329, B:A.410, B:W.411 pi-Stacking: B:W.411, B:W.411 Hydrophobic interactions: A:E.427

2 x XFH: 6-(2-{3-[2-(2-amino-6-methylpyridin-4-yl)ethyl]phenyl}ethyl)-4-methylpyridin-2-amine(Non-covalent)

XFH.7: 14 residues within 4Å: Chain A: P.298, V.300, N.302, F.317, S.318, G.319, W.320, Y.321, M.322, E.325, Y.439, Q.440 Ligands: HEM.1, ACT.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.298, A:V.300, A:F.317, A:Y.439, A:Y.439, A:Y.439 Hydrogen bonds: A:M.322, A:E.325 XFH.14: 14 residues within 4Å: Chain B: Q.211, P.298, V.300, N.302, M.303, F.317, G.319, W.320, Y.321, M.322, E.325, Y.439 Ligands: HEM.9, GOL.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.298, B:V.300, B:F.317, B:Y.439, B:Y.439 Hydrogen bonds: B:M.322, B:E.325 pi-Stacking: B:Y.439

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: C.58, C.63 Chain B: C.58, C.63 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.58, B:C.63, A:C.58, A:C.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delker, S.L. et al., Role of zinc in isoform-selective inhibitor binding to neuronal nitric oxide synthase . Biochemistry (2010)

Release Date

2011-02-09

Peptides

Nitric oxide synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase

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