SMTL ID : 3n5p.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: W.142, A.145, R.147, C.148, V.149, L.157, S.190, F.317, S.318, G.319, W.320, M.322, E.325, W.411, F.437, Y.439 Ligands: ACT.3, XFM.5, H4B.7 21 PLIP interactions: 21 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:L.157, A:L.157, A:F.317, A:F.317, A:F.317, A:W.320, A:E.325, A:F.437, A:F.437, A:F.437 Hydrogen bonds: A:Y.439 Water bridges: A:R.329 Salt bridges: A:R.147 pi-Stacking: A:W.142 Metal complexes: A:C.148 HEM.9: 18 residues within 4Å: Chain B: W.142, A.145, R.147, C.148, S.190, F.317, S.318, G.319, W.320, M.322, E.325, W.411, F.437, Y.439 Ligands: ACT.11, H4B.14, XFM.15, GOL.16 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.142, B:W.142, B:A.145, B:R.147, B:F.317, 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

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

ACT.2: 4 residues within 4Å: Chain A: Q.211, R.214, N.330, R.336 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, W.320, V.382, S.390 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.320, A:S.390 ACT.10: 5 residues within 4Å: Chain B: Q.211, R.214, N.330, R.336 Ligands: GOL.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.211, B:N.330, B:N.330 Salt bridges: B:R.214, B:R.336 ACT.11: 5 residues within 4Å: Chain B: G.150, 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: V.68, R.329, H.335, W.411 Chain B: W.38 Ligands: H4B.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.329, A:R.329 GOL.12: 5 residues within 4Å: Chain B: V.68, R.329, W.411 Ligands: H4B.14, GOL.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.329, B:R.329 GOL.16: 7 residues within 4Å: Chain B: V.68, W.411, Y.439 Ligands: HEM.9, ACT.10, GOL.12, XFM.15 No protein-ligand interaction detected (PLIP)

2 x XFM: 6-(2-{6-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-2-yl}ethyl)-4-methylpyridin-2-amine(Non-covalent)

XFM.5: 12 residues within 4Å: Chain A: P.298, V.300, N.302, M.303, F.317, S.318, G.319, W.320, Y.321, E.325, Y.439 Ligands: HEM.1 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 Hydrogen bonds: A:M.322, A:E.325 pi-Stacking: A:Y.439 XFM.15: 13 residues within 4Å: Chain B: 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.16 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.298, B:P.298, B:V.300, B:V.300, B:F.317, B:Y.439, B:Y.439 Hydrogen bonds: B:M.322, B:E.325

2 x CAD: CACODYLIC ACID(Non-covalent)

CAD.6: 3 residues within 4Å: Chain A: W.286, L.290, C.346 No protein-ligand interaction detected (PLIP) CAD.13: 4 residues within 4Å: Chain B: W.286, L.290, D.342, C.346 No protein-ligand interaction detected (PLIP)

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

H4B.7: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.329, A:R.329, A:A.410, A:W.411 pi-Stacking: A:W.411, A:W.411 H4B.14: 12 residues within 4Å: Chain A: W.409, F.424, H.425, Q.426, E.427 Chain B: S.66, V.68, R.329, A.410, W.411 Ligands: HEM.9, GOL.12 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.68, A:E.427 Hydrogen bonds: B:R.329, B:A.410, B:W.411 pi-Stacking: B:W.411, B:W.411

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: C.58, C.63 Chain B: C.58, C.63, G.65 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 ZN.17: 3 residues within 4Å: Chain A: E.39 Chain B: D.333, H.335 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.39, A:E.39, B:D.333, B:H.335, H2O.6

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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