SMTL ID : 4f8y.2 (1 other biounit)

Complex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 22 residues within 4Å: Chain A: H.9, S.14, F.15, N.16, E.18, P.82, I.83, W.84, W.85, S.86, T.127, H.128, N.129, T.130, Y.141, I.166, E.167, D.171, R.174 Chain B: L.47, R.55 Ligands: VK3.4 29 PLIP interactions: 24 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.84, A:W.84, B:L.47 Hydrogen bonds: A:F.15, A:N.16, A:N.16, A:I.83, A:I.83, A:W.85, A:S.86, A:T.127, A:T.127, A:N.129, A:T.130, A:Y.141, A:Y.141, A:E.167, A:E.167, A:D.171 Water bridges: A:R.174, B:R.55, B:R.55, B:R.55, B:R.55 Salt bridges: A:H.9 pi-Stacking: A:F.15, A:F.15, A:W.84, A:W.85 FAD.3: 25 residues within 4Å: Chain A: L.47, F.49, R.55, D.97 Chain B: H.9, S.14, F.15, N.16, E.18, P.82, I.83, W.84, W.85, S.86, T.127, H.128, N.129, T.130, Y.141, I.166, E.167, D.171, R.174, L.178 Ligands: VK3.2 27 PLIP interactions: 23 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.84, B:W.84, A:L.47, A:F.49 Hydrogen bonds: B:F.15, B:N.16, B:N.16, B:I.83, B:I.83, B:W.85, B:S.86, B:T.127, B:T.127, B:N.129, B:N.129, B:Y.141, B:E.167, B:E.167, A:R.55, A:R.55 Water bridges: B:N.11, B:Y.141, B:R.174, B:R.174, B:R.174 Salt bridges: B:H.9 pi-Stacking: B:W.84

2 x VK3: MENADIONE(Non-covalent)

VK3.2: 8 residues within 4Å: Chain A: R.55, Y.106, Y.108, L.113 Chain B: W.85, N.129, Y.141 Ligands: FAD.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.106, A:Y.108, A:L.113 Water bridges: B:N.129 VK3.4: 6 residues within 4Å: Chain A: W.85 Chain B: R.55, Y.106, Y.108, L.113 Ligands: FAD.1 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.108, B:L.113, A:W.85 pi-Stacking: A:W.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Complex structure of NADPH:quinone oxidoreductase with menadione in Streptococcus mutans. TO BE PUBLISHED

Release Date

2012-06-06

Peptides

NADPH Quinone Oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

NADPH Quinone Oxidoreductase

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