SMTL ID : 3n65.1

Structure of neuronal nitric oxide synthase S602H 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 1.80 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: H4B.2, ACT.3, XFJ.4, XFJ.9 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:F.408, A:F.408 Water bridges: A:R.118, A:R.300 Salt bridges: A:R.300 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.10: 23 residues within 4Å: Chain B: 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: H4B.11, ACT.12, XFJ.14, XFJ.15 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, B:R.118, B:L.128, B:F.288, B:F.288, B:F.288, B:F.288, 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

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

H4B.2: 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.9 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.381, A:W.382 Water bridges: A:S.38, A:I.39 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: A:W.382 Hydrophobic interactions: B:E.398 H4B.11: 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.10, XFJ.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.381, B:W.382 Water bridges: B:S.38 pi-Stacking: B:W.382, B:W.382 pi-Cation interactions: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.291, A:S.361 ACT.12: 4 residues within 4Å: Chain B: G.121, W.291, V.353 Ligands: HEM.10 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.124, B:Q.124, B:S.361

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

XFJ.4: 16 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 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: 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 Water bridges: A:R.185 XFJ.9: 14 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, H4B.2, CL.5, ZN.7 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.381, A:W.382, B:W.380, B:F.395, B:F.395 Hydrogen bonds: A:V.384, B:W.10 pi-Stacking: A:W.382, B:W.10 XFJ.14: 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.10, MTL.13 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:W.10, B:L.41, B:P.269, B:F.288, B:W.382, B:Y.410 Hydrogen bonds: B:R.118, B:Q.182, B:E.296 Water bridges: B:N.273 XFJ.15: 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: ZN.8, HEM.10, H4B.11, MTL.13, CL.16 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:V.384 pi-Stacking: A:W.10, B:W.382

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.9 Ligand excluded by PLIP CL.16: 7 residues within 4Å: Chain A: S.390, F.395, H.396 Chain B: R.300, D.304 Ligands: ZN.8, XFJ.15 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: 4 residues within 4Å: Chain A: D.304 Chain B: H.396 Ligands: CL.5, XFJ.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.396, A:D.304, A:D.304 ZN.8: 4 residues within 4Å: Chain A: H.396 Chain B: D.304 Ligands: XFJ.15, CL.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.304, B:D.304, A:H.396

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

MTL.13: 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.14, XFJ.15 13 PLIP interactions: 13 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:A.201, B:V.203, B:D.413, B:D.413, B:D.413

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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