SMTL ID : 2npx.2 (1 other biounit)

NADH BINDING SITE AND CATALYSIS OF NADH PEROXIDASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 33 residues within 4Å: Chain A: L.6, G.7, S.9, H.10, G.11, E.32, K.33, S.41, C.42, T.77, E.78, I.79, S.110, P.111, G.112, A.113, M.131, R.132, I.160, E.163, N.247, W.250, G.280, D.281, A.297, L.298, A.299, T.300, A.302 Chain B: F.424, Q.425, P.426 Ligands: NAD.2 31 PLIP interactions: 26 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.160, A:I.160 Hydrogen bonds: A:S.9, A:H.10, A:H.10, A:G.11, A:K.33, A:K.33, A:I.79, A:I.79, A:A.113, A:D.281, A:A.297, A:A.299, A:T.300, B:F.424 Water bridges: A:S.9, A:S.9, A:S.9, A:R.132, A:R.132, A:R.132, A:N.247, A:A.282, A:A.302, B:F.424, B:F.424, B:F.424, B:Q.425 Salt bridges: A:R.132 pi-Cation interactions: A:K.33 FAD.3: 33 residues within 4Å: Chain A: F.424, Q.425, P.426 Chain B: L.6, G.7, S.9, H.10, G.11, E.32, K.33, S.41, C.42, T.77, E.78, I.79, S.110, P.111, G.112, A.113, M.131, R.132, I.160, E.163, N.247, W.250, G.280, D.281, A.297, L.298, A.299, T.300, A.302 Ligands: NAD.4 31 PLIP interactions: 26 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.160, B:I.160 Hydrogen bonds: B:S.9, B:H.10, B:H.10, B:G.11, B:K.33, B:K.33, B:I.79, B:I.79, B:A.113, B:D.281, B:A.297, B:A.299, B:T.300, A:F.424 Water bridges: B:S.9, B:S.9, B:S.9, B:R.132, B:R.132, B:R.132, B:N.247, B:A.282, B:A.302, A:F.424, A:F.424, A:F.424, A:Q.425 Salt bridges: B:R.132 pi-Cation interactions: B:K.33

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 21 residues within 4Å: Chain A: L.118, I.155, G.156, S.157, G.158, Y.159, I.160, E.163, D.179, I.180, L.181, Y.188, A.241, V.242, G.243, A.297, L.298, G.328 Chain B: F.424, Q.425 Ligands: FAD.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.159, A:Y.159, A:I.160 Hydrogen bonds: A:S.157, A:Y.159, A:I.160, A:G.161, A:I.180, A:Y.188, A:Y.188, A:G.243, A:A.297, A:G.328 Water bridges: A:S.157, A:G.158, A:G.158, A:L.185, A:V.214, A:G.328 NAD.4: 21 residues within 4Å: Chain A: F.424, Q.425 Chain B: L.118, I.155, G.156, S.157, G.158, Y.159, I.160, E.163, D.179, I.180, L.181, Y.188, A.241, V.242, G.243, A.297, L.298, G.328 Ligands: FAD.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.159, B:Y.159, B:I.160 Hydrogen bonds: B:S.157, B:Y.159, B:I.160, B:G.161, B:I.180, B:Y.188, B:Y.188, B:G.243, B:A.297, B:G.328 Water bridges: B:S.157, B:G.158, B:G.158, B:L.185, B:V.214, B:G.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stehle, T. et al., NADH binding site and catalysis of NADH peroxidase. Eur.J.Biochem. (1993)

Release Date

1994-01-31

Peptides

NADH PEROXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NADH PEROXIDASE

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