SMTL ID : 2qx8.1

Crystal Structure of Quinone Reductase II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 26 residues within 4Å: Chain A: H.11, K.15, S.16, F.17, N.18, S.20, P.102, L.103, Y.104, W.105, F.106, T.147, T.148, G.149, G.150, Y.155, P.192, E.193, R.200, K.201, V.204 Chain B: N.66, Y.67, G.68, D.117 Ligands: ML2.2 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.104, A:Y.104, A:Y.104, B:Y.67 Hydrogen bonds: A:F.17, A:N.18, A:N.18, A:S.20, A:S.20, A:L.103, A:L.103, A:W.105, A:F.106, A:T.147, A:T.147, A:G.149, A:G.150, A:Y.155, A:Y.155, B:N.66 Water bridges: A:H.11, A:N.161 Salt bridges: A:H.11 FAD.7: 26 residues within 4Å: Chain A: N.66, Y.67, G.68, D.117 Chain B: H.11, K.15, S.16, F.17, N.18, S.20, P.102, L.103, Y.104, W.105, F.106, T.147, T.148, G.149, G.150, Y.155, E.193, E.197, R.200, K.201, V.204 Ligands: ML2.8 24 PLIP interactions: 21 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.104, B:Y.104, B:Y.104, A:Y.67 Hydrogen bonds: B:F.17, B:N.18, B:N.18, B:S.20, B:S.20, B:L.103, B:L.103, B:W.105, B:F.106, B:T.147, B:T.147, B:G.149, B:G.150, B:Y.155, B:E.193, A:N.66 Water bridges: B:N.161, B:E.193, A:N.66 Salt bridges: B:H.11

2 x ML2: N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide(Non-covalent)

ML2.2: 10 residues within 4Å: Chain A: W.105, F.106, G.149, G.150 Chain B: Q.122, F.126, I.128, G.174, F.178 Ligands: FAD.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.155 pi-Stacking: A:W.105 Hydrophobic interactions: B:F.178, B:F.178 ML2.8: 11 residues within 4Å: Chain A: Q.122, F.126, G.174, F.178 Chain B: W.105, F.106, G.149, G.150, M.154 Ligands: CL.5, FAD.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.178, A:F.178 pi-Stacking: B:W.105

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.173, H.177, C.222, T.223 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.173, A:H.177, A:C.222, A:C.222 ZN.9: 3 residues within 4Å: Chain B: H.173, H.177, C.222 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.173, B:H.177, B:C.222, H2O.19

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

CL.4: 1 residues within 4Å: Chain A: T.213 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: D.127, I.128 Ligands: ML2.8 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: D.40, A.43, M.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.40 GOL.10: 5 residues within 4Å: Chain A: N.45, R.49 Chain B: N.45, E.47, R.49 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.45, B:N.45, B:E.47, B:R.49, B:R.49, A:N.45, A:R.49, A:R.49 Water bridges: A:N.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calamini, B. et al., Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2. Biochem.J. (2008)

Release Date

2008-09-02

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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