SMTL ID : 5buc.1

Oxidized quinone reductase 2 in complex with ethidium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 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.7: 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: 25 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 Chain B: N.66, Y.67, G.68, D.117 Ligands: ET.4 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:R.200, B:N.66 Water bridges: A:E.197, A:K.201, A:K.201 Salt bridges: A:H.11 pi-Stacking: A:F.17, A:F.17 FAD.8: 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: ET.3 24 PLIP interactions: 22 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: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:R.200, A:N.66 Water bridges: B:H.11, B:N.161 Salt bridges: B:H.11 pi-Stacking: B:W.105

3 x ET: ETHIDIUM(Non-covalent)

ET.3: 19 residues within 4Å: Chain A: N.66, G.68, V.69, T.71, H.72, L.120, C.121, Q.122, F.126, I.128, F.178 Chain B: W.105, G.149, G.150, N.161, E.193, I.194 Ligands: ET.6, FAD.8 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.122, A:F.126, A:F.126, A:F.178 Hydrogen bonds: A:G.68, A:T.71, A:Q.122 Water bridges: B:Y.155, B:N.161 ET.4: 18 residues within 4Å: Chain A: W.105, F.106, G.149, G.150, M.154, Y.155, N.161, I.194 Chain B: G.68, L.120, Q.122, F.126, I.128, F.131, Y.132, G.174, F.178 Ligands: FAD.2 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:W.105, B:F.126, B:F.126, B:I.128, B:I.128 Hydrogen bonds: A:N.161, B:Y.132, B:Y.132 pi-Stacking: A:W.105, B:F.178 Water bridges: B:G.68, B:T.71, B:T.71, B:Q.122 ET.6: 8 residues within 4Å: Chain A: I.128, F.131 Chain B: G.149, G.150, T.151, M.154, I.194 Ligands: ET.3 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.194, A:I.128, A:F.131

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

SO4.5: 3 residues within 4Å: Chain A: S.196, E.197, R.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.197 Salt bridges: A:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leung, K.K. et al., Structure of quinone reductase 2 in complex with DNA intercalating agents. to be published

Release Date

2016-06-15

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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