SMTL ID : 7q5y.1 (3 other biounits)

Structure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

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

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: H.99, D.102, C.103, C.106, K.108, A.109, C.112, Q.115, R.153, V.208, G.209 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.99, A:C.103, A:C.106, A:C.112 SF4.2: 13 residues within 4Å: Chain A: Y.149, C.154, V.155, V.156, C.157, Y.158, R.159, C.160, C.206, P.207, V.208, A.210, I.211 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.154, A:C.157, A:C.160, A:C.206 SF4.3: 10 residues within 4Å: Chain A: C.232, L.234, C.235, V.237, G.238, C.239, I.267, C.268, K.270, V.385 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.232, A:C.235, A:C.239, A:C.268 SF4.4: 9 residues within 4Å: Chain A: C.164, T.170, M.191, C.196, E.197, M.198, C.199, G.200, C.202 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.164, A:C.196, A:C.199, A:C.202 SF4.7: 12 residues within 4Å: Chain C: I.181, T.346, C.347, G.348, Q.349, C.350, C.353, S.391, I.392, C.393, L.395, G.396 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.347, C:C.350, C:C.353, C:C.393 SF4.8: 14 residues within 4Å: Chain D: H.58, C.97, P.98, L.102, F.103, M.122, C.127, L.128, F.129, C.130, G.131, L.132, C.133, M.144 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.97, D:C.127, D:C.130, D:C.133 SF4.9: 13 residues within 4Å: Chain D: H.60, C.87, V.88, A.89, C.90, Y.91, M.92, C.93, F.120, C.137, P.138, C.141, L.142 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.87, D:C.90, D:C.93, D:C.137 SF4.11: 14 residues within 4Å: Chain B: R.257 Chain F: A.34, C.35, C.36, G.71, T.72, G.98, G.99, C.100, P.106, F.107, G.128, C.129, P.130 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.35, F:C.36, F:C.100, F:C.129

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

FES.5: 9 residues within 4Å: Chain A: Y.35, C.37, Y.38, G.46, A.47, C.48, R.49, C.51, C.65 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.37, A:C.48, A:C.51, A:C.65 FES.10: 9 residues within 4Å: Chain E: C.86, S.88, V.90, C.91, C.127, L.128, G.129, A.130, C.131 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.86, E:C.91, E:C.127, E:C.131

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.6: 19 residues within 4Å: Chain C: G.65, R.66, G.67, A.69, K.76, N.92, D.94, E.95, S.96, Y.180, G.183, E.184, E.185, V.218, N.219, N.220, T.223, G.394, L.395 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.180, C:Y.180, C:E.184, C:L.395 Hydrogen bonds: C:R.66, C:G.67, C:N.92, C:D.94, C:E.95, C:S.96, C:G.183, C:E.185, C:N.219, C:N.220, C:N.220, C:T.223 Water bridges: C:N.92, C:N.92 Salt bridges: C:K.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warkentin, E. et al., Structure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus. To Be Published

Release Date

2022-11-16

Peptides

NADH dehydrogenase I chain G: A
NADH-quinone oxidoreductase subunit C/D 2: B
NADH-quinone oxidoreductase subunit F: C
NADH-quinone oxidoreductase subunit I: D
NADH-quinone oxidoreductase subunit E: E
NADH-quinone oxidoreductase subunit B: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NADH dehydrogenase I chain G

NADH-quinone oxidoreductase subunit C/D 2

NADH-quinone oxidoreductase subunit F

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit E

NADH-quinone oxidoreductase subunit B

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