SMTL ID : 3n64.1

Structure of neuronal nitric oxide synthase D597N mutant heme domain in complex with 6,6'-(2,2'-(5-amino-1,3-phenylene)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: 18 residues within 4Å: Chain A: W.113, R.118, C.119, V.120, G.121, L.128, S.161, F.288, S.289, G.290, W.291, M.293, E.296, R.300, W.382, F.408, Y.410 Ligands: XFN.2 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, 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:W.382, A:F.408, A:F.408 Hydrogen bonds: A:E.296, A:Y.410 Water bridges: A:R.118, A:R.300, A:R.300 Salt bridges: A:R.118, A:R.300 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.10: 20 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, V.120, G.121, S.161, F.288, S.289, G.290, W.291, M.293, E.296, R.300, V.353, W.382, F.408, Y.410 Ligands: XFN.11, ACT.12 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:W.113, B:A.116, B:R.118, 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 Salt bridges: B:R.118, B:R.300 pi-Stacking: B:W.113 Metal complexes: B:C.119

2 x XFN: 6,6'-[(5-aminobenzene-1,3-diyl)diethane-2,1-diyl]bis(4-methylpyridin-2-amine)(Non-covalent)

XFN.2: 15 residues within 4Å: Chain A: M.40, Q.182, R.185, P.269, V.271, F.288, W.291, Y.292, E.296, R.300, V.381, W.382 Chain B: F.395 Ligands: HEM.1, CL.7 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.269, A:V.271, A:F.288, A:W.382, A:W.382, A:W.382, B:F.395, B:F.395 Hydrogen bonds: A:E.296 Water bridges: A:Q.182, A:Q.182, A:R.185, A:R.185, B:H.396 pi-Stacking: A:W.382 pi-Cation interactions: A:R.300 XFN.11: 16 residues within 4Å: Chain A: W.10, F.395 Chain B: M.40, Q.182, R.185, P.269, V.271, F.288, W.291, Y.292, E.296, R.300, V.381, W.382 Ligands: HEM.10, CL.13 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.269, B:V.271, B:F.288, B:W.382, B:W.382, B:W.382, A:F.395, A:F.395 Hydrogen bonds: B:E.296 Water bridges: B:Q.182, B:R.185, B:R.185, B:R.185, A:H.396 pi-Stacking: B:W.382 pi-Cation interactions: B:R.300

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

ACT.3: 5 residues within 4Å: Chain A: G.121, Q.124, W.291, V.353, S.361 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.124, 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.10 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.124, B:S.361

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.5: 5 residues within 4Å: Chain A: R.300, D.304 Chain B: S.390, H.396 Ligands: CL.7 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.396, A:D.304, A:D.304, H2O.13 ZN.6: 5 residues within 4Å: Chain A: S.390, H.396 Chain B: R.300, D.304 Ligands: CL.13 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.396, B:D.304, B:D.304, H2O.5

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

CL.7: 5 residues within 4Å: Chain A: R.300, D.304 Chain B: H.396 Ligands: XFN.2, ZN.5 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: Q.182, Y.292, R.300, N.301 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: Q.182, Y.292, R.300, N.301 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: H.396 Chain B: R.300, D.304 Ligands: ZN.6, XFN.11 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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