SMTL ID : 5lbu.1

Structure of the human quinone reductase 2 (NQO2) in complex with to CL097

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.174, H.178, C.223 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.174, A:H.178, A:C.223, A:C.223 ZN.8: 3 residues within 4Å: Chain B: H.174, H.178, C.223 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.174, B:H.178, B:C.223, B:C.223

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

FAD.2: 27 residues within 4Å: Chain A: H.12, K.16, S.17, F.18, N.19, S.21, P.103, L.104, Y.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, P.193, E.194, E.198, R.201, K.202, V.205 Chain B: N.67, Y.68, G.69, D.118 Ligands: C09.5 26 PLIP interactions: 24 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.105, A:Y.105, A:Y.105, B:Y.68 Hydrogen bonds: A:F.18, A:N.19, A:N.19, A:S.21, A:S.21, A:L.104, A:L.104, A:W.106, A:F.107, A:T.148, A:T.148, A:G.150, A:G.151, A:Y.156, A:Y.156, A:E.194, A:R.201, A:K.202, B:N.67 Salt bridges: A:H.12 pi-Stacking: A:F.18, A:F.18 FAD.7: 27 residues within 4Å: Chain A: N.67, Y.68, G.69, D.118 Chain B: H.12, K.16, S.17, F.18, N.19, S.21, P.103, L.104, Y.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, P.193, E.194, E.198, R.201, K.202, V.205 Ligands: C09.6 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.105, B:Y.105, B:Y.105, A:Y.68 Hydrogen bonds: B:F.18, B:N.19, B:N.19, B:S.21, B:S.21, B:L.104, B:W.106, B:F.107, B:T.148, B:T.148, B:G.150, B:G.151, B:Y.156 Salt bridges: B:H.12 pi-Stacking: B:F.18, B:W.106 Water bridges: A:N.67

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

SO4.3: 2 residues within 4Å: Chain A: S.197, E.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.197, A:S.197, A:E.199 SO4.4: 4 residues within 4Å: Chain A: E.48, R.50 Chain B: E.48, R.50 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.46, B:E.48 Salt bridges: B:R.50, A:R.50 SO4.9: 3 residues within 4Å: Chain B: T.57, A.82, S.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.83 Water bridges: B:D.84, B:D.84 SO4.10: 2 residues within 4Å: Chain B: R.32 Ligands: C09.12 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.32 SO4.11: 3 residues within 4Å: Chain B: P.15, N.24 Ligands: C09.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.24 Water bridges: B:K.23 Salt bridges: B:K.23

4 x C09: 2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-4-amine(Non-covalent)

C09.5: 10 residues within 4Å: Chain A: W.106, G.150, G.151, M.155, N.162 Chain B: F.127, I.129, F.132, F.179 Ligands: FAD.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.162 Water bridges: A:Y.156, A:N.162 pi-Stacking: A:W.106 Hydrophobic interactions: B:F.127, B:F.132, B:F.179 C09.6: 10 residues within 4Å: Chain A: Q.123, F.127, I.129, F.179 Chain B: W.106, G.150, G.151, M.155, N.162 Ligands: FAD.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.129, A:F.179 C09.12: 4 residues within 4Å: Chain B: D.28, S.31 Ligands: SO4.10, C09.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.28 Water bridges: B:D.28 C09.13: 6 residues within 4Å: Chain B: K.23, N.24, V.27, D.28 Ligands: SO4.11, C09.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.27 Hydrogen bonds: B:N.24, B:D.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gross, C. et al., Imiquimod Inhibits Mitochondrial Complex I and Induces K+ efflux-independent Nlrp3 Inflammasome Activation via Nek7. To Be Published

Release Date

2016-07-27

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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