SMTL ID : 3n62.1

Structure of neuronal nitric oxide synthase D597N mutant heme domain in complex 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 1.95 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: W.113, A.116, R.118, C.119, V.120, G.121, L.128, S.161, M.274, F.288, S.289, G.290, W.291, M.293, E.296, R.300, V.353, W.382, F.408 Ligands: XFJ.2, ACT.3, H4B.10, XFJ.11 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:A.116, A:L.128, A:F.288, A:F.288, A:F.288, A:F.288, A:W.291, A:E.296, A:V.353, A:W.382, A:F.408, A:F.408 Water bridges: A:R.118 Salt bridges: A:R.300 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.12: 22 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, V.120, G.121, S.161, M.274, F.288, S.289, G.290, W.291, M.293, E.296, R.300, V.353, W.382, F.408 Ligands: H4B.8, XFJ.13, XFJ.14, ACT.15 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, B:F.288, B:F.288, B:F.288, B:F.288, B:W.291, B:W.291, B:E.296, B:V.353, B:W.382, B:F.408, B:F.408 Hydrogen bonds: B:R.118 Salt bridges: B:R.300 pi-Stacking: B:W.113 Metal complexes: B:C.119

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

XFJ.2: 17 residues within 4Å: Chain A: M.40, L.41, R.118, Q.182, P.269, V.271, F.288, G.290, W.291, Y.292, E.296, R.300, W.382, Y.410 Chain B: W.10 Ligands: HEM.1, MTL.4 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.41, A:P.269, A:F.288, A:W.382, A:Y.410, B:W.10 Hydrogen bonds: A:R.118, A:Q.182, A:E.296 XFJ.11: 15 residues within 4Å: Chain A: R.300, D.304, V.381, W.382, V.384 Chain B: W.10, D.13, W.380, F.395, H.396 Ligands: HEM.1, MTL.4, CL.5, ZN.7, H4B.10 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.380, B:F.395, B:F.395, A:V.381, A:W.382 Hydrogen bonds: B:W.10, A:W.382 pi-Stacking: B:W.10, A:W.382 XFJ.13: 17 residues within 4Å: Chain A: W.10 Chain B: M.40, L.41, R.118, Q.182, P.269, V.271, F.288, G.290, W.291, Y.292, E.296, R.300, W.382, Y.410 Ligands: HEM.12, MTL.16 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.41, B:P.269, B:F.288, B:W.382, B:Y.410, A:W.10 Hydrogen bonds: B:R.118, B:Q.182, B:E.296 Water bridges: B:R.185, B:N.273, B:N.273 XFJ.14: 15 residues within 4Å: Chain A: W.10, D.13, W.380, F.395, H.396 Chain B: R.300, D.304, V.381, W.382, V.384 Ligands: H4B.8, ZN.9, HEM.12, MTL.16, CL.17 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.380, A:F.395, A:F.395, B:V.381, B:W.382 Hydrogen bonds: A:W.10, B:W.382 pi-Stacking: A:W.10, B:W.382

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

ACT.3: 5 residues within 4Å: Chain A: G.121, W.291, V.353, S.361 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.291 Hydrogen bonds: A:W.291, A:S.361 ACT.15: 4 residues within 4Å: Chain B: G.121, W.291, V.353 Ligands: HEM.12 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.124, B:S.361

2 x MTL: D-MANNITOL(Non-covalent)

MTL.4: 12 residues within 4Å: Chain A: S.181, R.185, A.201, N.202, V.203, Q.204, F.205, N.273, D.413, W.415 Ligands: XFJ.2, XFJ.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.181, A:R.185, A:Q.204, A:F.205, A:N.273, A:D.413 Water bridges: A:R.185, A:A.201 MTL.16: 12 residues within 4Å: Chain B: S.181, R.185, A.201, N.202, V.203, Q.204, F.205, N.273, D.413, W.415 Ligands: XFJ.13, XFJ.14 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.181, B:R.185, B:N.202, B:Q.204, B:F.205, B:N.273, B:D.413 Water bridges: B:S.181, B:N.273, B:D.413

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 7 residues within 4Å: Chain A: R.300, D.304 Chain B: S.390, F.395, H.396 Ligands: ZN.7, XFJ.11 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain A: S.390, F.395, H.396 Chain B: R.300, D.304 Ligands: ZN.9, XFJ.14 Ligand excluded by PLIP

3 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: C.30, C.35, M.36 Chain B: C.30, C.35, M.36 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.30, B:C.35, A:C.30, A:C.35 ZN.7: 5 residues within 4Å: Chain A: R.300, D.304 Chain B: H.396 Ligands: CL.5, XFJ.11 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.304, A:D.304, B:H.396, H2O.1 ZN.9: 4 residues within 4Å: Chain A: H.396 Chain B: D.304 Ligands: XFJ.14, CL.17 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.304, B:D.304, A:H.396, H2O.7

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

H4B.8: 11 residues within 4Å: Chain A: W.380, F.395, H.396, Q.397, E.398 Chain B: S.38, M.40, V.381, W.382 Ligands: HEM.12, XFJ.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.381, B:W.382 pi-Stacking: B:W.382, B:W.382 H4B.10: 11 residues within 4Å: Chain A: S.38, M.40, V.381, W.382 Chain B: W.380, F.395, H.396, Q.397, E.398 Ligands: HEM.1, XFJ.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.382 Water bridges: A:S.38 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: A:W.382

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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