SMTL ID : 5eai.3 (6 other biounits)

Crystal Structure of NAD(P)H dehydrogenase, quinone 1 complexed with a chemotherapeutic naphthoquinone E6a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 24 residues within 4Å: Chain A: H.15, T.19, S.20, F.21, N.22, A.24, P.106, L.107, Q.108, W.109, F.110, T.151, T.152, G.153, G.154, Y.159, I.196, R.204, L.208 Chain B: N.68, Q.70, Y.71, P.72, E.121 22 PLIP interactions: 17 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.108, B:Y.71, B:P.72, B:E.121 Hydrogen bonds: A:F.21, A:N.22, A:N.22, A:L.107, A:L.107, A:W.109, A:F.110, A:T.151, A:T.151, A:G.153, A:G.154, A:Y.159, A:Y.159, A:R.204, B:N.68, B:Q.70 Salt bridges: A:H.15 pi-Stacking: A:F.21 FAD.3: 24 residues within 4Å: Chain A: Q.70, Y.71, P.72, E.121 Chain B: H.15, T.19, S.20, F.21, N.22, A.24, P.106, L.107, Q.108, W.109, F.110, T.151, T.152, G.153, G.154, Y.159, I.196, R.204, L.208 Ligands: E6A.2 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Q.108, A:Y.71, A:E.121 Hydrogen bonds: B:F.21, B:N.22, B:N.22, B:L.107, B:L.107, B:W.109, B:F.110, B:T.151, B:T.151, B:G.153, B:G.154, B:Y.159, B:R.204, A:Q.70 Salt bridges: B:H.15 pi-Stacking: B:F.21, B:F.21

1 x E6A: (2~{R},3~{R})-2-[(2~{S},3~{S})-3-bromanyl-1,4-bis(oxidanylidene)-2,3-dihydronaphthalen-2-yl]-3-oxidanyl-2,3-dihydronaphthalene-1,4-dione(Non-covalent)

E6A.2: 10 residues within 4Å: Chain A: P.72, A.73, Y.130, Y.132, F.182 Chain B: W.109, F.110, G.153, G.154 Ligands: FAD.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.72, A:A.73, A:Y.130, A:F.182, B:F.110 pi-Stacking: B:W.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pidugu, L.S. et al., A direct interaction between NQO1 and a chemotherapeutic dimeric naphthoquinone. Bmc Struct.Biol. (2016)

Release Date

2016-02-17

Peptides

NAD(P)H dehydrogenase [quinone] 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

NAD(P)H dehydrogenase [quinone] 1

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