SMTL ID : 4fgj.1

Oxidized quinone reductase 2 in complex with primaquine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.176, H.180, C.225, T.226 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.176, A:H.180, A:C.225, A:C.225 ZN.6: 3 residues within 4Å: Chain B: H.176, H.180, C.225 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.176, B:H.180, B:C.225, B:C.225

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

FAD.2: 28 residues within 4Å: Chain A: H.14, K.18, S.19, F.20, N.21, S.23, P.105, L.106, Y.107, W.108, F.109, T.150, T.151, G.152, G.153, Y.158, P.195, E.196, E.200, R.203, K.204, V.207 Chain B: V.67, N.69, Y.70, G.71, D.120 Ligands: 1PQ.3 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.107, A:Y.107, A:Y.107, B:Y.70 Hydrogen bonds: A:F.20, A:N.21, A:N.21, A:S.23, A:L.106, A:L.106, A:W.108, A:F.109, A:T.150, A:G.152, A:G.153, A:Y.158, A:E.196, A:R.203, B:N.69 Water bridges: A:H.14, A:H.14, A:N.164 Salt bridges: A:H.14 pi-Stacking: A:F.20, A:F.20 FAD.7: 28 residues within 4Å: Chain A: V.67, N.69, Y.70, G.71, D.120 Chain B: H.14, K.18, S.19, F.20, N.21, S.23, P.105, L.106, Y.107, W.108, F.109, T.150, T.151, G.152, G.153, Y.158, P.195, E.196, E.200, R.203, K.204, V.207 Ligands: 1PQ.4 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.107, B:Y.107, B:Y.107, A:Y.70 Hydrogen bonds: B:F.20, B:N.21, B:N.21, B:S.23, B:L.106, B:W.108, B:F.109, B:T.150, B:T.150, B:T.151, B:G.152, B:G.153, B:Y.158, B:E.196, A:N.69 Water bridges: B:H.14, B:H.14, B:N.164 Salt bridges: B:H.14

2 x 1PQ: (4S)-N~4~-(6-methoxyquinolin-8-yl)pentane-1,4-diamine(Non-covalent)

1PQ.3: 12 residues within 4Å: Chain A: W.108, F.109, G.152, G.153, M.157, Y.158, N.164 Chain B: F.129, I.131, G.177, F.181 Ligands: FAD.2 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.131, B:F.181, A:W.108, A:F.109 pi-Stacking: B:F.181 Water bridges: A:Y.158, A:N.164 1PQ.4: 12 residues within 4Å: Chain A: F.129, Y.135, G.177, F.181 Chain B: W.108, F.109, G.152, G.153, Y.158, N.164, E.196 Ligands: FAD.7 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.108, B:F.109, A:F.181 Hydrogen bonds: B:E.196 Water bridges: B:Y.158, B:N.164 pi-Stacking: A:F.181

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain B: D.166, R.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.166 Water bridges: B:S.167 GOL.8: 6 residues within 4Å: Chain B: E.50, K.56, D.57, A.84, D.86, R.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.86, B:R.121 Water bridges: B:T.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leung, K.K. et al., Crystal structures of quinone reductase 2 bound to antimalarial drugs reveal conformational change upon reduction. J.Biol.Chem. (2013)

Release Date

2013-03-13

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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