SMTL ID : 3jx2.1

Structure of rat neuronal nitric oxide synthase D597N/M336V mutant heme domain in complex with N1-{(3'S,4'S)-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}-N2-(3'-fluorophenethyl)ethane-1,2-diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 22 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, V.353, W.382, F.408, Y.410 Ligands: H4B.2, JI4.3, ACT.4 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:W.113, A:A.116, A:R.118, A:V.120, A:L.128, A:F.288, A:F.288, A:F.288, A:W.291, A:E.296, A:V.353, A:F.408, A:F.408 Hydrogen bonds: A:R.118, A:Y.410 Water bridges: A:R.300 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.7: 18 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, V.120, S.161, M.274, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: H4B.8, JI4.9 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, B:V.120, B:F.288, B:F.288, B:F.288, B:W.291, B:E.296, B:F.408, B:F.408 Water bridges: B:R.300 Salt bridges: B:R.118 pi-Stacking: B:W.113 Metal complexes: B:C.119

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

H4B.2: 12 residues within 4Å: Chain A: S.38, V.40, R.300, V.381, W.382 Chain B: W.380, F.395, H.396, Q.397, E.398 Ligands: HEM.1, GOL.5 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:E.398 Hydrogen bonds: A:R.300, A:V.381, A:W.382 Water bridges: A:S.38, A:W.382 pi-Stacking: A:W.382, A:W.382 H4B.8: 12 residues within 4Å: Chain A: W.380, F.395, H.396, Q.397, E.398 Chain B: S.38, V.40, R.300, V.381, W.382 Ligands: HEM.7, GOL.11 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.300, B:V.381, B:W.382 pi-Stacking: B:W.382, B:W.382 pi-Cation interactions: B:W.382 Hydrophobic interactions: A:E.398

2 x JI4: N-{(3S,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-[2-(3-fluorophenyl)ethyl]ethane-1,2-diamine(Non-covalent)

JI4.3: 16 residues within 4Å: Chain A: V.40, L.41, Q.182, P.269, V.271, F.288, G.290, W.291, Y.292, M.293, E.296, W.382, Y.410 Chain B: W.10 Ligands: HEM.1, GOL.5 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.269, A:F.288, A:W.382, B:W.10, B:W.10 Hydrogen bonds: A:M.293, A:E.296, A:E.296 Water bridges: A:Q.182, A:N.301 pi-Stacking: A:Y.410 JI4.9: 16 residues within 4Å: Chain A: W.10 Chain B: V.40, L.41, Q.182, P.269, V.271, F.288, S.289, G.290, W.291, Y.292, E.296, W.382, Y.410 Ligands: HEM.7, GOL.11 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.269, B:F.288, B:W.382, B:Y.410, A:W.10, A:W.10 Hydrogen bonds: B:E.296, B:E.296 Water bridges: B:Q.182, B:N.301 pi-Stacking: B:Y.410

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

ACT.4: 6 residues within 4Å: Chain A: G.121, I.123, W.291, V.353, S.361 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.291 ACT.10: 5 residues within 4Å: Chain B: G.121, Q.124, W.291, V.353, S.361 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.124 Water bridges: B:Q.124

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: R.300, D.304, W.382 Chain B: W.10 Ligands: H4B.2, JI4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.300, A:R.300, A:D.304 GOL.11: 6 residues within 4Å: Chain A: W.10, H.396 Chain B: R.300, W.382 Ligands: H4B.8, JI4.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.396, B:R.300

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.30, C.35 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delker, S.L. et al., Unexpected binding modes of nitric oxide synthase inhibitors effective in the prevention of a cerebral palsy phenotype in an animal model. J.Am.Chem.Soc. (2010)

Release Date

2010-05-05

Peptides

Nitric oxide synthase, brain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase, brain

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