SMTL ID : 8rfm.1

Human NOQ1 enzyme in complex with NADH by serial crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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: I.51, N.65, Q.67, Y.68, P.69, E.118 23 PLIP interactions: 17 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Q.105, A:Q.105, B:I.51, B:Y.68, 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:Y.156, A:R.201, B:N.65, B:N.65, B:Q.67 Salt bridges: A:H.12 pi-Stacking: A:F.18 FAD.3: 25 residues within 4Å: Chain A: N.65, Q.67, Y.68, P.69, E.118 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: NAD.2 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.105, B:Q.105, A:Y.68, A:E.118 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:N.65, A:N.65, A:Q.67 Salt bridges: B:H.12 FAD.4: 23 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: N.65, Q.67, P.69, E.118 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Q.105, C:Q.105, D:E.118 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:N.65 Salt bridges: C:H.12 FAD.6: 26 residues within 4Å: Chain C: I.51, N.65, Q.67, Y.68, P.69, E.118 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: NAD.5 21 PLIP interactions: 5 interactions with chain C, 16 interactions with chain D Hydrophobic interactions: C:I.51, C:Y.68, C:E.118, D:Q.105, D:Q.105 Hydrogen bonds: C:N.65, C:Q.67, 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:Y.156, D:R.201 Salt bridges: D:H.12

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 7 residues within 4Å: Chain A: Y.129, F.233, Q.234 Chain B: M.155, H.162, H.195 Ligands: FAD.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.162 Salt bridges: B:H.195 Hydrophobic interactions: A:Y.129 pi-Stacking: A:Y.129 NAD.5: 10 residues within 4Å: Chain C: P.69, Y.127, Y.129, F.179, F.233, Q.234 Chain D: G.150, H.162, H.195 Ligands: FAD.6 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:H.195, D:H.195 Hydrogen bonds: C:Y.129, C:Y.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grieco, A. et al., Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations. Protein Sci. (2024)

Release Date

2024-05-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NAD(P)H dehydrogenase [quinone] 1

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