SMTL ID : 4zvl.1

Oxidized quinone reductase 2 in complex with acridine orange

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

3 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: 4 residues within 4Å: Chain A: H.72, K.76, G.123, D.127 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.72, A:D.127, A:D.127, H2O.5 ZN.6: 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: 28 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: V.64, N.66, Y.67, G.68, D.117 Ligands: AO.5 25 PLIP interactions: 23 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: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:N.161, A:E.193, A:E.193 Salt bridges: A:H.11 pi-Stacking: A:F.17 FAD.7: 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: AO.3 28 PLIP interactions: 26 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, A:N.66 Water bridges: B:H.11, B:H.11, B:R.200, B:R.200, B:R.200, B:K.201 Salt bridges: B:H.11 pi-Stacking: B:F.17

2 x AO: ACRIDINE ORANGE(Non-covalent)

AO.3: 15 residues within 4Å: Chain A: G.68, Q.122, F.126, I.128, Y.132, G.174, F.178 Chain B: W.105, F.106, G.149, Y.155, N.161, E.193, I.194 Ligands: FAD.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.126, A:F.126, A:I.128, A:F.178, A:F.178, B:W.105 AO.5: 15 residues within 4Å: Chain A: W.105, F.106, G.149, Y.155, N.161, E.193, I.194 Chain B: G.68, Q.122, F.126, I.128, Y.132, G.174, F.178 Ligands: FAD.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.178, B:F.178, A:W.105

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

2016-04-06

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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