SMTL ID : 8ok0.1

Crystal structure of human NQO1 in complex with the inhibitor PMSF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 25 residues within 4Å: Chain A: H.12, T.16, S.17, F.18, N.19, A.21, P.103, L.104, Q.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, I.193, R.201, L.205 Chain B: Q.67, Y.68, P.69, E.118 Ligands: ACE.4, PMS.6 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Q.105, A:Q.105, B:Y.68, B:P.69, B:E.118 Hydrogen bonds: A:F.18, A:N.19, A:N.19, 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:R.201, B:Q.67 Water bridges: A:T.16, A:G.194, A:R.201 Salt bridges: A:H.12 pi-Stacking: A:F.18, A:F.18 FAD.5: 25 residues within 4Å: Chain A: Q.67, Y.68, P.69 Chain B: H.12, T.16, S.17, F.18, N.19, A.21, P.103, L.104, Q.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, I.193, R.201, I.202, L.205 Ligands: PMS.2, GOL.7 24 PLIP interactions: 22 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.105, B:Q.105, A:Y.68 Hydrogen bonds: B:F.18, B:N.19, B:N.19, B:L.104, B:W.106, B:F.107, B:T.148, B:T.148, B:G.150, B:G.151, B:Y.156, B:Y.156, B:R.201, A:Q.67 Water bridges: B:T.16, B:A.21, B:G.194, B:R.201 Salt bridges: B:H.12 pi-Stacking: B:F.18, B:F.18 FAD.9: 25 residues within 4Å: Chain C: H.12, T.16, S.17, F.18, N.19, A.21, P.103, L.104, Q.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, I.193, R.201, L.205 Chain D: Q.67, Y.68, P.69 Ligands: GOL.11, PMS.13, PMS.15 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Q.105, C:Q.105, D:Y.68, D:P.69 Hydrogen bonds: C:F.18, C:N.19, C:N.19, C:L.104, C:W.106, C:F.107, C:T.148, C:T.148, C:G.150, C:G.151, C:Y.156, C:Y.156, C:R.201, D:Q.67, D:Q.67 Water bridges: C:A.21, C:I.193, C:R.201 Salt bridges: C:H.12 pi-Stacking: C:F.18, C:F.18 FAD.14: 24 residues within 4Å: Chain C: Q.67, Y.68, P.69 Chain D: H.12, T.16, S.17, F.18, N.19, A.21, P.103, L.104, Q.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, I.193, R.201, L.205 Ligands: PMS.10, GOL.17 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Q.105, D:Q.105, C:Y.68, C:P.69 Hydrogen bonds: D:F.18, D:N.19, D:N.19, D:L.104, D:W.106, D:F.107, D:T.148, D:T.148, D:G.150, D:G.151, D:Y.156, D:R.201, C:Q.67 Water bridges: D:A.21, D:R.201 Salt bridges: D:H.12 pi-Stacking: D:F.18, D:F.18

5 x PMS: phenylmethanesulfonic acid(Covalent)(Non-covalent)

PMS.2: 9 residues within 4Å: Chain A: Y.127, Y.129, F.179 Chain B: W.106, F.107, G.151, M.155, H.162 Ligands: FAD.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.127, A:Y.127, A:F.179, B:F.107 pi-Stacking: B:W.106 PMS.6: 8 residues within 4Å: Chain A: W.106, G.151, Y.156, H.162 Chain B: Y.127, Y.129, F.179 Ligands: FAD.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.127, B:F.179, B:F.179 pi-Stacking: A:W.106 PMS.10: 10 residues within 4Å: Chain C: Y.127, Y.129, F.179 Chain D: W.106, F.107, G.150, G.151, Y.156, H.162 Ligands: FAD.14 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.127, C:F.179, C:F.179, D:F.107 pi-Stacking: D:W.106 PMS.13: 8 residues within 4Å: Chain C: G.150, G.151, M.155, Y.156, H.162 Chain D: Y.129 Ligands: FAD.9, PMS.15 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.129 Hydrogen bonds: D:Y.129, C:G.151, C:Y.156 Salt bridges: C:H.162 PMS.15: 7 residues within 4Å: Chain C: W.106, F.107 Chain D: P.69, Y.127, F.179 Ligands: FAD.9, PMS.13 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.107, C:F.107, D:Y.127, D:F.179, D:F.179 pi-Stacking: C:W.106 Hydrogen bonds: D:Y.127

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: K.142, W.216, E.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.142, A:K.142, A:E.218 GOL.7: 8 residues within 4Å: Chain A: I.51, F.66, Y.68 Chain B: H.12, S.13, Y.43, Q.105 Ligands: FAD.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.13, B:S.13 Water bridges: B:A.11, A:Y.68, A:Y.68 GOL.11: 8 residues within 4Å: Chain C: H.12, S.13, Y.43 Chain D: I.51, S.52, F.66, Y.68 Ligands: FAD.9 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Water bridges: D:Y.68, C:Q.105, C:Q.105 Hydrogen bonds: C:S.13, C:S.13 GOL.16: 4 residues within 4Å: Chain D: Y.222, P.225, L.228, E.247 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.222, D:E.247 GOL.17: 9 residues within 4Å: Chain C: I.51, F.66, Y.68 Chain D: H.12, S.13, E.14, Y.43, Q.105 Ligands: FAD.14 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.13, D:S.13 Water bridges: D:A.11, D:Y.43, D:Q.105, C:Y.68 GOL.18: 4 residues within 4Å: Chain A: N.46 Chain D: Y.43, A.44, N.46 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 2 interactions with chain A Water bridges: B:N.48 Hydrogen bonds: D:N.46, D:N.46, A:N.46, A:N.46

3 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.4: 2 residues within 4Å: Chain A: R.201 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) ACE.8: 2 residues within 4Å: Chain B: K.33, G.34 No protein-ligand interaction detected (PLIP) ACE.12: 4 residues within 4Å: Chain C: Q.244, E.247, K.248, L.260 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.247, C:L.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grieco, A. et al., Structural dynamics at the active site of the cancer-associated flavoenzyme NQO1 probed by chemical modification with PMSF. Febs Lett. (2023)

Release Date

2023-11-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

NAD(P)H dehydrogenase [quinone] 1