SMTL ID : 9mqx.1

Electron-bifurcating Tungstopyranopterin-containing aldehyde oxidoreductase with NADH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

hetero-1-1-1-3-3-mer

Ligands

20 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)

SF4.1: 10 residues within 4Å: Chain A: C.138, I.146, C.168, I.169, G.170, C.171, G.172, C.174, I.194, W.195 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.138, A:C.168, A:C.171, A:C.174 SF4.2: 13 residues within 4Å: Chain A: C.128, V.129, R.130, C.131, D.132, R.133, C.134, I.157, V.177, C.178, T.180, Y.182, I.183 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.128, A:C.131, A:C.134, A:C.178 SF4.5: 12 residues within 4Å: Chain B: V.303, S.474, C.475, G.476, K.477, C.478, C.481, A.519, L.520, C.521, L.523, G.524 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.475, B:C.478, B:C.481, B:C.521 SF4.10: 11 residues within 4Å: Chain B: I.563, C.568, I.569, G.570, C.571, G.572, C.574, H.591, C.608, T.610, I.613 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:H.591 Metal complexes: B:C.568, B:C.571, B:C.574, B:C.608 SF4.11: 10 residues within 4Å: Chain B: C.578, P.579, I.583, C.598, I.599, G.600, C.601, G.602, Q.603, C.604 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.578, B:C.598, B:C.601, B:C.604 SF4.13: 11 residues within 4Å: Chain D: S.73, R.76, R.181, A.286, C.287, C.290, S.292, C.294, C.489, F.491 Ligands: PTE.14 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.287, D:C.290, D:C.294, D:C.489 SF4.17: 12 residues within 4Å: Chain E: C.52, Q.54, C.55, A.58, P.59, C.60, C.94, P.95, F.96, N.98, M.99, K.110 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.52, E:C.55, E:C.60, E:C.94 SF4.18: 10 residues within 4Å: Chain E: C.64, A.66, A.68, L.69, C.84, I.85, C.87, R.88, C.90, A.108 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.64, E:C.84, E:C.87, E:C.90 SF4.19: 14 residues within 4Å: Chain E: C.12, V.13, G.14, C.15, G.16, S.17, C.18, V.39, P.49, C.124, P.125, T.126, A.128, L.129 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.12, E:C.15, E:C.18, E:C.124 SF4.20: 13 residues within 4Å: Chain E: L.5, C.22, K.26, R.36, V.37, T.51, C.111, D.112, Q.113, C.114, P.118, Y.119, C.120 5 PLIP interactions: 5 interactions with chain E, Salt bridges: E:D.112 Metal complexes: E:C.22, E:C.111, E:C.114, E:C.120 SF4.21: 12 residues within 4Å: Chain F: S.73, R.76, R.181, A.286, C.287, C.290, S.292, A.293, C.294, C.489, F.491 Ligands: PTE.22 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.287, F:C.290, F:C.294, F:C.489 SF4.25: 12 residues within 4Å: Chain G: C.52, Q.54, C.55, A.58, P.59, C.60, V.77, C.94, F.96, N.98, M.99, K.110 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.52, G:C.55, G:C.60, G:C.94 SF4.26: 9 residues within 4Å: Chain G: C.64, A.68, L.69, C.84, I.85, C.87, R.88, C.90, A.108 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.64, G:C.84, G:C.87, G:C.90 SF4.27: 13 residues within 4Å: Chain G: C.12, V.13, C.15, G.16, S.17, C.18, V.39, P.49, C.124, P.125, T.126, A.128, L.129 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.12, G:C.15, G:C.18, G:C.124 SF4.28: 13 residues within 4Å: Chain G: L.5, C.22, K.26, R.36, V.37, T.51, C.111, D.112, Q.113, C.114, P.118, Y.119, C.120 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.112 Metal complexes: G:C.22, G:C.111, G:C.114, G:C.120 SF4.29: 13 residues within 4Å: Chain H: S.73, R.76, R.181, A.286, C.287, C.290, S.292, A.293, C.294, G.295, C.489, F.491 Ligands: PTE.30 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.287, H:C.290, H:C.294, H:C.489 SF4.33: 13 residues within 4Å: Chain I: C.52, Q.54, C.55, A.58, P.59, C.60, V.77, C.94, F.96, N.98, M.99, K.110, F.145 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.52, I:C.55, I:C.60, I:C.94 SF4.34: 9 residues within 4Å: Chain I: C.64, A.66, A.68, L.69, C.84, I.85, C.87, C.90, A.108 2 PLIP interactions: 2 interactions with chain I, Metal complexes: I:C.64, I:C.84 SF4.35: 14 residues within 4Å: Chain I: C.12, V.13, G.14, C.15, G.16, S.17, C.18, V.39, P.49, F.123, C.124, P.125, T.126, L.129 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.12, I:C.15, I:C.18, I:C.124 SF4.36: 13 residues within 4Å: Chain I: L.5, C.22, K.26, R.36, V.37, T.51, C.111, D.112, Q.113, C.114, P.118, Y.119, C.120 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:D.112 Metal complexes: I:C.22, I:C.111, I:C.114, I:C.120

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.3: 11 residues within 4Å: Chain A: T.35, L.36, C.37, H.38, G.46, N.47, C.48, R.49, C.51, I.66, C.68 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.37, A:C.48, A:C.51, A:C.68 FES.8: 9 residues within 4Å: Chain B: C.33, G.35, G.37, C.38, C.69, H.70, G.71, F.72, C.73 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.33, B:C.38, B:C.69, B:C.73 FES.12: 10 residues within 4Å: Chain C: C.77, G.79, A.81, C.82, C.118, L.119, G.120, C.121, C.122, V.127 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.77, C:C.82, C:C.118, C:C.122

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.204, C.207, C.230, C.233 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.204, A:C.207, A:C.230, A:C.233 ZN.9: 4 residues within 4Å: Chain B: C.458, H.545, C.550, C.555 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.458, B:H.545, B:H.545, B:C.550, B:C.555

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.6: 19 residues within 4Å: Chain B: G.186, R.187, G.188, K.197, N.214, D.216, E.217, G.218, F.302, G.305, E.306, S.307, L.340, N.341, N.342, T.345, G.522, L.523 Ligands: NAI.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.302, B:F.302, B:E.306, B:L.523 Hydrogen bonds: B:R.187, B:G.188, B:N.214, B:D.216, B:G.218, B:G.305, B:E.306, B:S.307, B:L.340, B:N.342 Salt bridges: B:K.197

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.7: 18 residues within 4Å: Chain B: G.188, G.189, G.190, F.192, K.197, E.217, G.218, D.219, F.302, E.306, H.327, T.329, L.340, S.420, M.444, G.446, S.447 Ligands: FMN.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.302, B:F.302 Hydrogen bonds: B:K.197, B:E.217, B:G.218, B:D.219, B:L.340 pi-Stacking: B:F.192, B:F.192, B:H.327

3 x PTE: TUNGSTOPTERIN COFACTOR(Non-covalent)(Covalent)

PTE.14: 23 residues within 4Å: Chain D: R.76, S.92, N.93, S.94, G.95, C.174, R.181, A.182, A.183, G.184, R.185, E.311, N.336, M.340, P.342, R.440, V.445, D.484, F.488, L.490 Ligands: SF4.13, MG.15, MG.16 19 PLIP interactions: 19 interactions with chain D, Hydrogen bonds: D:R.76, D:R.76, D:S.92, D:N.93, D:S.94, D:G.95, D:A.182, D:A.182, D:G.184, D:G.184, D:N.336, D:N.336, D:F.488, D:L.490 Salt bridges: D:R.76, D:R.181, D:R.440, D:D.484 Metal complexes: D:N.93 PTE.22: 26 residues within 4Å: Chain F: R.76, S.92, N.93, S.94, G.95, C.174, R.181, A.182, A.183, G.184, R.185, E.309, E.311, N.336, M.340, D.341, P.342, R.440, V.445, D.484, F.488, C.489, L.490 Ligands: SF4.21, MG.23, MG.24 17 PLIP interactions: 17 interactions with chain F, Hydrogen bonds: F:R.76, F:S.92, F:N.93, F:G.95, F:A.182, F:G.184, F:G.184, F:E.309, F:E.309, F:N.336, F:N.336, F:F.488, F:L.490 Salt bridges: F:R.76, F:R.181, F:R.440, F:D.484 PTE.30: 26 residues within 4Å: Chain H: R.76, S.92, N.93, S.94, G.95, C.174, M.176, R.181, A.182, A.183, G.184, R.185, E.311, N.332, C.335, N.336, M.340, P.342, R.440, V.445, D.484, F.488, L.490 Ligands: SF4.29, MG.31, MG.32 17 PLIP interactions: 17 interactions with chain H, Hydrogen bonds: H:R.76, H:N.93, H:N.93, H:S.94, H:G.95, H:A.182, H:R.185, H:C.335, H:N.336, H:F.488, H:L.490 Salt bridges: H:R.76, H:R.181, H:R.440, H:D.484 Metal complexes: H:N.93, H:A.182

6 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 2 residues within 4Å: Chain D: H.180 Ligands: PTE.14 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain D: N.78, A.91, N.93, R.446 Ligands: PTE.14 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain F: A.91, N.93, R.440, R.446 Ligands: PTE.22 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain F: R.181, E.306, E.309 Ligands: PTE.22 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:E.309, F:E.309, PTE.22 MG.31: 5 residues within 4Å: Chain H: A.91, N.93, R.440, R.446 Ligands: PTE.30 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain H: H.180, E.306, N.336 Ligands: PTE.30 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, X. et al., An electron-bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-07-16

Peptides

NADH:ubiquinone oxidoreductase chain G-like protein: A
NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit: B
NADH:ubiquinone oxidoreductase 24 kD subunit: C
Aldehyde:ferredoxin oxidoreductase: DFH
Fe-S-cluster-containing hydrogenase subunit: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
I

NADH:ubiquinone oxidoreductase chain G-like protein

NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit

NADH:ubiquinone oxidoreductase 24 kD subunit

Aldehyde:ferredoxin oxidoreductase

Fe-S-cluster-containing hydrogenase subunit