SMTL ID : 4zvm.1

Oxidized quinone reductase 2 in complex with doxorubicin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.173, H.177, C.222 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.173, A:H.177, A:C.222, A:C.222 ZN.4: 3 residues within 4Å: Chain B: H.173, H.177, C.222 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.173, B:H.177, B:C.222, B:C.222

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

FAD.2: 27 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, E.197, R.200, K.201, V.204 Chain B: N.66, Y.67, G.68, D.117 Ligands: DM2.3 29 PLIP interactions: 27 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.104, 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, A:R.200, B:N.66 Water bridges: A:H.11, A:H.11, A:H.11, A:E.193 Salt bridges: A:H.11 pi-Stacking: A:F.17, A:F.17 FAD.5: 27 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, P.192, E.193, E.197, R.200, K.201, V.204 Ligands: DM2.6 27 PLIP interactions: 25 interactions with chain B, 2 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:Y.155, B:K.201 Water bridges: B:H.11, B:K.15, B:E.193, B:R.200, B:R.200, A:N.66 Salt bridges: B:H.11

2 x DM2: DOXORUBICIN(Non-covalent)

DM2.3: 17 residues within 4Å: Chain A: W.105, F.106, G.149, G.150, T.151, M.154, N.161, E.193, I.194 Chain B: V.69, H.72, Q.122, F.126, I.128, G.174, F.178 Ligands: FAD.2 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:W.105, A:I.194 Hydrogen bonds: A:N.161, B:Q.122, B:Q.122 Water bridges: B:H.72, B:H.72, B:Q.122 pi-Stacking: B:F.178 DM2.6: 19 residues within 4Å: Chain A: N.66, V.69, H.72, Q.122, F.126, I.128, G.174, F.178 Chain B: W.105, F.106, G.149, G.150, T.151, M.154, N.161, A.191, E.193, I.194 Ligands: FAD.5 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.105, B:F.106, B:I.194 Hydrogen bonds: B:N.161, B:E.193 Water bridges: A:H.72, A:Q.122 pi-Stacking: A:F.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leung, K.K. et al., Binding of DNA-Intercalating Agents to Oxidized and Reduced Quinone Reductase 2. Biochemistry (2015)

Release Date

2016-03-30

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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