SMTL ID : 3n5t.1

Structure of endothelial nitric oxide synthase heme domain complexed with 6,6'-(2,2'-(pyridine-3,5-diyl)bis(ethane-2,1-diyl))bis(4-methylpyridin-2-amine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: W.142, A.145, R.147, C.148, V.149, S.190, F.317, S.318, G.319, W.320, M.322, E.325, W.411, F.437 Ligands: ACT.2, XFJ.4, H4B.5 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:F.317, A:F.317, 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 Water bridges: A:E.325, A:R.329 pi-Stacking: A:W.142 Metal complexes: A:C.148 HEM.8: 19 residues within 4Å: Chain B: W.142, A.145, R.147, C.148, V.149, G.150, S.190, M.303, F.317, S.318, G.319, W.320, M.322, E.325, W.411, F.437 Ligands: ACT.9, XFJ.11, H4B.12 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.142, B:W.142, B:W.142, B:A.145, B:F.317, B:F.317, B:F.317, B:F.317, B:W.320, B:E.325, B:F.437, B:F.437 pi-Stacking: B:W.142 Metal complexes: B:C.148

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

ACT.2: 4 residues within 4Å: Chain A: 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.9: 7 residues within 4Å: Chain B: G.150, I.152, Q.153, W.320, V.382, S.390 Ligands: HEM.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.153, B:W.320 Hydrogen bonds: B:S.390, B:S.390

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: R.329, H.335 Chain B: W.38 Ligands: XFJ.4, H4B.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.329, A:R.329, A:H.335 GOL.10: 5 residues within 4Å: Chain A: W.38 Chain B: V.68, R.329, H.335 Ligands: H4B.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.329, B:R.329, B:H.335 Water bridges: B:D.333

2 x XFJ: 6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine)(Non-covalent)

XFJ.4: 17 residues within 4Å: Chain A: V.68, L.69, R.147, Q.211, P.298, V.300, F.317, S.318, G.319, W.320, Y.321, M.322, E.325, Y.439 Chain B: W.38 Ligands: HEM.1, GOL.3 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.68, A:P.298, A:F.317, A:Y.439, A:Y.439, B:W.38 Hydrogen bonds: A:R.147, A:Q.211, A:M.322, A:E.325 Water bridges: A:Y.295 XFJ.11: 15 residues within 4Å: Chain A: W.38 Chain B: V.68, L.69, R.147, Q.211, P.298, V.300, F.317, G.319, W.320, Y.321, M.322, E.325, Y.439 Ligands: HEM.8 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.68, B:P.298, B:F.317, B:Y.439, B:Y.439, A:W.38 Hydrogen bonds: B:R.147, B:Q.211, B:M.322, B:E.325

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

H4B.5: 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.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.329, A:A.410, A:W.411 Water bridges: A:S.66, A:W.411 pi-Stacking: A:W.411, A:W.411 pi-Cation interactions: A:W.411 Hydrophobic interactions: B:E.427 H4B.12: 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.8, GOL.10 7 PLIP interactions: 6 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 pi-Cation interactions: B:W.411 Hydrophobic interactions: A:E.427

2 x CAD: CACODYLIC ACID(Non-covalent)

CAD.6: 2 residues within 4Å: Chain A: L.290, C.346 No protein-ligand interaction detected (PLIP) CAD.13: 2 residues within 4Å: Chain B: W.286, C.346 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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

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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