SMTL ID : 4xdh.1

Crystal Structure of Quinone Reductase II in complex with a 2-(4-methoxy-phenyl)-5-methoxy-indol-3-one molecule

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.174, H.178, C.223, T.224 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.178, A:C.223, A:C.223 ZN.7: 3 residues within 4Å: Chain B: H.174, H.178, C.223 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.223, B:C.223

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

FAD.2: 25 residues within 4Å: Chain A: H.12, K.16, S.17, F.18, N.19, S.21, P.103, L.104, Y.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, P.193, E.194, R.201, K.202 Chain B: N.67, Y.68, G.69, D.118 Ligands: 3ZV.3 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.105, A:Y.105, A:Y.105, A:Y.105, B:Y.68 Hydrogen bonds: A:F.18, A:N.19, A:N.19, A:S.21, A:S.21, A:L.104, A:L.104, A:W.106, A:F.107, A:T.148, A:T.148, A:G.150, A:G.151, A:Y.156, A:Y.156, A:R.201, B:N.67 Water bridges: A:N.162, A:N.162 Salt bridges: A:H.12 FAD.8: 24 residues within 4Å: Chain A: N.67, Y.68, G.69, D.118 Chain B: H.12, K.16, S.17, F.18, N.19, S.21, P.103, L.104, Y.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, P.193, E.194, R.201 Ligands: 3ZV.9 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.105, B:Y.105, B:Y.105, A:Y.68 Hydrogen bonds: B:F.18, B:N.19, B:N.19, B:S.21, B:S.21, B:L.104, B:L.104, B:W.106, B:F.107, B:T.148, B:T.148, B:G.150, B:G.151, B:Y.156, B:E.194, B:R.201 Salt bridges: B:H.12 pi-Stacking: B:F.18

2 x 3ZV: 5-methoxy-2-(4-methoxyphenyl)-3H-indol-3-one(Non-covalent)

3ZV.3: 9 residues within 4Å: Chain A: W.106, G.150, G.151, M.155, I.195 Chain B: F.127, I.129, F.179 Ligands: FAD.2 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.127, B:I.129, B:I.129, B:F.179, A:I.195 Water bridges: A:N.162 3ZV.9: 9 residues within 4Å: Chain A: F.127, I.129, F.179 Chain B: W.106, G.150, G.151, M.155, I.195 Ligands: FAD.8 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.127, A:I.129, A:I.129, A:I.129, A:F.179, B:I.195 Water bridges: B:N.162

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: S.197, E.198, E.199, R.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.198 Salt bridges: A:R.201 SO4.5: 4 residues within 4Å: Chain A: E.48, R.50 Chain B: E.48, R.50 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.50, B:R.50 Hydrogen bonds: B:E.48 Water bridges: B:N.46 SO4.6: 6 residues within 4Å: Chain A: E.48, K.54, D.55, A.82, D.84, R.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.84 Salt bridges: A:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cassagnes, L.E. et al., Role of Quinone Reductase 2 in the Antimalarial Properties of Indolone-Type Derivatives. Molecules (2017)

Release Date

2016-01-13

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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