SMTL ID : 3n61.1

Structure of neuronal nitric oxide synthase D597N/M336V 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

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: W.113, A.116, R.118, C.119, V.120, 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, H4B.3, ACT.4 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:A.116, A:R.118, 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 Hydrogen bonds: A:R.118 Water bridges: A:R.300 Salt bridges: A:R.300 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.9: 20 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, V.120, G.121, M.274, F.288, S.289, G.290, W.291, M.293, E.296, R.300, V.353, W.382, F.408 Ligands: XFJ.10, H4B.11, ACT.12 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, B:R.118, B:V.120, B:F.288, B:F.288, B:F.288, B:F.288, B:W.291, B:E.296, B:V.353, B:F.408, B:F.408 Hydrogen bonds: B:R.118 Water bridges: B:R.300 Salt bridges: B:R.300 pi-Stacking: B:W.113 Metal complexes: B:C.119

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

XFJ.2: 14 residues within 4Å: Chain A: V.40, L.41, R.118, Q.182, P.269, V.271, F.288, G.290, W.291, Y.292, E.296, R.300 Chain B: W.10 Ligands: HEM.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.40, A:L.41, A:P.269, A:F.288, B:W.10 Hydrogen bonds: A:R.118, A:Q.182, A:M.293, A:E.296, A:R.300 XFJ.10: 15 residues within 4Å: Chain A: W.10 Chain B: V.40, L.41, R.118, Q.182, P.269, V.271, F.288, G.290, W.291, Y.292, E.296, R.300, Y.410 Ligands: HEM.9 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.40, B:L.41, B:P.269, B:F.288, B:Y.410, A:W.10 Hydrogen bonds: B:R.118, B:Q.182, B:M.293, B:E.296, B:R.300 Water bridges: B:R.185, B:R.185, B:N.273

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

H4B.3: 11 residues within 4Å: Chain A: S.38, V.40, V.381, W.382 Chain B: W.380, F.395, H.396, Q.397, E.398 Ligands: HEM.1, CL.6 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.381, A:W.382 Water bridges: A:R.300, A:R.300, A:R.300, A:R.300 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, V.40, V.381, W.382 Ligands: HEM.9, CL.13 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.381, B:W.382 Water bridges: B:R.300, B:R.300, B:R.300, B:R.300 pi-Stacking: B:W.382, B:W.382 Hydrophobic interactions: A:E.398

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

ACT.4: 5 residues within 4Å: Chain A: I.123, 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.12: 4 residues within 4Å: Chain B: G.121, W.291, V.353 Ligands: HEM.9 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.124, B:S.361

3 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: C.30, C.35, M.36 Chain B: C.30, C.35 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.30, A:C.35, B:C.30, B:C.35 ZN.8: 5 residues within 4Å: Chain A: R.300, D.304 Chain B: H.396 Ligands: CL.6, CL.7 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.15: 5 residues within 4Å: Chain A: H.396 Chain B: R.300, D.304 Ligands: CL.13, CL.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.304, B:D.304, A:H.396

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

CL.6: 6 residues within 4Å: Chain A: R.300, D.304 Chain B: H.396 Ligands: H4B.3, CL.7, ZN.8 Ligand excluded by PLIP CL.7: 7 residues within 4Å: Chain A: R.300, D.304 Chain B: S.390, F.395, H.396 Ligands: CL.6, ZN.8 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: R.300, D.304 Ligands: H4B.11, CL.14, ZN.15 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain A: S.390, F.395 Chain B: R.300, D.304 Ligands: CL.13, ZN.15 Ligand excluded by PLIP

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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