SMTL ID : 5fuq.1

CRYSTAL STRUCTURE OF THE H80R VARIANT OF NQO1 BOUND TO DICOUMAROL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 23 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 Ligands: DTC.2 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Q.105, A:Q.105, B:Y.68, B:P.69 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:Y.156, A:R.201, B:Q.67 Water bridges: A:T.16, A:A.21, B:F.66 Salt bridges: A:H.12 FAD.6: 23 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, L.205 Ligands: DTC.7 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.105, B:Q.105, A:Y.68, A:P.69 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:T.16, B:T.16, B:A.21, A:F.66 Salt bridges: B:H.12 pi-Stacking: B:F.18

3 x DTC: BISHYDROXY[2H-1-BENZOPYRAN-2-ONE,1,2-BENZOPYRONE](Non-covalent)

DTC.2: 13 residues within 4Å: Chain A: W.106, F.107, G.150, G.151, M.155, H.162 Chain B: Y.127, Y.129, F.179, F.233, F.237 Ligands: FAD.1, DTC.3 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.127, B:Y.127, B:Y.129, B:Y.129, B:F.179, B:F.179, B:F.233, B:F.237, A:F.107 Salt bridges: A:H.162, A:H.195 pi-Stacking: A:W.106 DTC.3: 6 residues within 4Å: Chain A: G.150, S.192, H.195 Chain B: F.233, Q.234 Ligands: DTC.2 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.233, B:F.233, B:F.233, B:F.233, B:Q.234 Water bridges: A:S.192 Salt bridges: A:H.195 pi-Stacking: A:H.195 DTC.7: 14 residues within 4Å: Chain A: Y.127, Y.129, M.132, F.179, F.233, F.237 Chain B: W.106, F.107, G.150, G.151, M.155, H.162, H.195 Ligands: FAD.6 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.127, A:Y.127, A:Y.129, A:Y.129, A:F.179, A:F.233, A:F.237, A:F.237, B:F.107 Water bridges: A:Y.129, A:Y.129, B:S.152 pi-Stacking: A:Y.129, B:W.106 Salt bridges: B:H.162, B:H.195

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: Y.127, T.128, Y.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.129 ACT.5: 5 residues within 4Å: Chain A: H.12, S.13, Q.105 Chain B: I.51, Y.68 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.13, A:S.13 Water bridges: A:Q.105, B:Y.68 Salt bridges: A:H.12 Hydrophobic interactions: B:Y.68 ACT.8: 4 residues within 4Å: Chain A: Y.68 Chain B: H.12, S.13, Q.105 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.13, B:Y.43, B:Q.105 Salt bridges: B:H.12 Hydrophobic interactions: A:Y.68 ACT.9: 4 residues within 4Å: Chain B: E.124, Y.127, T.128, Y.129 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.129 Hydrogen bonds: B:E.124, B:Y.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medina-Carmona, E. et al., Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution. Hum.Mol.Genet. (2017)

Release Date

2017-02-22

Peptides

NAD(P)H DEHYDROGENASE [QUINONE] 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD(P)H DEHYDROGENASE [QUINONE] 1