SMTL ID : 7z7t.1

Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: I.179, P.197, S.350, C.351, G.352, W.353, C.354, C.357, T.396, F.397, C.398, H.400 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.351, A:C.354, A:C.357, A:C.398 SF4.5: 12 residues within 4Å: Chain C: H.99, D.102, C.103, C.106, E.108, G.109, C.112, L.114, Q.115, T.203, G.204 Chain D: I.512 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.99, C:C.103, C:C.106, C:C.112 SF4.6: 13 residues within 4Å: Chain C: C.151, I.152, A.153, C.154, Y.155, R.156, C.157, F.181, C.201, P.202, T.203, V.205, F.206 5 PLIP interactions: 5 interactions with chain C, pi-Cation interactions: C:F.181 Metal complexes: C:C.151, C:C.154, C:C.157, C:C.201 SF4.7: 11 residues within 4Å: Chain C: C.228, Q.230, C.231, I.233, G.234, C.235, L.262, C.263, R.265, G.266, R.388 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.228, C:C.231, C:C.235, C:C.263 SF4.10: 14 residues within 4Å: Chain D: R.250, R.270, H.355 Chain E: S.62, C.63, C.64, G.100, T.101, A.128, C.129, Y.136, G.157, C.158, P.159 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.63, E:C.64, E:C.129, E:C.158 SF4.11: 14 residues within 4Å: Chain F: I.48, C.70, P.71, V.72, C.74, I.75, C.99, I.100, F.101, C.102, G.103, L.104, C.105, L.116 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.70, F:C.99, F:C.102, F:C.105 SF4.12: 13 residues within 4Å: Chain F: C.60, V.61, A.62, C.63, N.64, L.65, C.66, L.77, F.92, C.109, P.110, T.111, I.114 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.60, F:C.63, F:C.66, F:C.109

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 19 residues within 4Å: Chain A: G.61, R.62, G.63, K.72, N.90, D.92, E.93, M.94, Y.178, G.181, E.182, E.183, V.216, N.217, N.218, T.221, A.399, H.400 Ligands: NAI.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.178, A:E.182, A:A.399, A:H.400 Hydrogen bonds: A:G.63, A:N.90, A:N.90, A:E.93, A:M.94, A:G.181, A:E.183, A:N.217, A:N.218, A:N.218, A:T.221 Salt bridges: A:K.72

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

NAI.3: 17 residues within 4Å: Chain A: G.63, G.64, A.65, F.67, K.72, L.75, E.93, M.94, E.95, Y.178, E.183, K.200, F.203, R.320, T.323, A.399 Ligands: FMN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.95, A:Y.178 Hydrogen bonds: A:K.72, A:M.94, A:E.95, A:E.183, A:R.320, A:R.320 Salt bridges: A:K.200, A:K.200 pi-Stacking: A:F.67, A:F.203

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

FES.4: 10 residues within 4Å: Chain B: C.92, S.94, V.96, C.97, C.133, L.134, G.135, N.136, C.137, N.142 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.92, B:C.97, B:C.133, B:C.137 FES.8: 12 residues within 4Å: Chain C: L.20, Y.32, C.34, W.35, G.43, A.44, C.45, R.46, Q.47, C.48, M.65, C.67 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.34, C:C.45, C:C.48, C:C.67

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain C: D.617, Q.632, E.647, D.729, D.731 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.617, C:E.647, C:D.731

8 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.13: 17 residues within 4Å: Chain G: I.33, L.37, F.44, Y.49 Chain H: I.89, D.111, L.112, N.113, I.114, F.118, L.125 Chain I: H.13, F.16, A.17, L.20, I.24 Ligands: 3PE.15 18 PLIP interactions: 7 interactions with chain H, 7 interactions with chain I, 4 interactions with chain G Hydrophobic interactions: H:I.89, H:I.89, H:L.112, H:I.114, H:F.118, I:F.16, I:F.16, I:A.17, I:L.20, I:I.24, G:I.33, G:L.37, G:F.44, G:F.44 Hydrogen bonds: H:N.113, H:N.113 Salt bridges: I:H.13, I:H.13 3PE.15: 14 residues within 4Å: Chain G: M.1, F.3, A.4, I.7, C.8, I.11, L.37, A.38, G.41, F.44, S.45, Y.49 Chain I: H.13 Ligands: 3PE.13 9 PLIP interactions: 8 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: G:F.3, G:A.4, G:A.4, G:I.7, G:L.37, G:F.44 Hydrogen bonds: G:M.1, G:Y.49 Salt bridges: I:H.13 3PE.16: 12 residues within 4Å: Chain J: I.8, I.9, L.12, V.16, L.64, W.65, T.66, F.77 Chain K: L.477, F.480, Y.481 Ligands: LFA.19 20 PLIP interactions: 13 interactions with chain J, 7 interactions with chain K Hydrophobic interactions: J:I.8, J:I.8, J:I.9, J:L.12, J:L.12, J:V.16, J:L.64, J:W.65, J:W.65, J:F.77, J:F.77, K:L.477, K:F.480, K:F.480, K:F.480, K:Y.481, K:Y.481 Hydrogen bonds: J:T.66, J:T.66, K:Y.481 3PE.17: 18 residues within 4Å: Chain J: M.569, N.570, A.573, R.577 Chain K: T.169, K.173, I.176, Y.177, A.180, I.229, V.233, L.240 Chain L: L.289, V.416, I.420, Y.423 Ligands: 3PE.20, 3PE.21 17 PLIP interactions: 4 interactions with chain L, 4 interactions with chain J, 9 interactions with chain K Hydrophobic interactions: L:L.289, L:I.420, L:Y.423, L:Y.423, J:A.573, J:R.577, K:K.173, K:I.176, K:I.176, K:Y.177, K:Y.177, K:Y.177, K:A.180, K:I.229, K:V.233 Salt bridges: J:R.577, J:R.577 3PE.18: 18 residues within 4Å: Chain J: A.165, M.168, K.169, V.172, V.173, V.176, F.180, P.234, L.235, Y.545, F.549, V.550, F.553, L.554 Chain K: F.306, F.427, V.434, R.442 19 PLIP interactions: 16 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: J:M.168, J:K.169, J:K.169, J:V.172, J:V.173, J:V.176, J:F.180, J:P.234, J:L.235, J:Y.545, J:F.549, J:F.549, J:F.549, J:F.549, J:V.550, J:F.553, K:F.427, K:V.434 Salt bridges: K:R.442 3PE.20: 10 residues within 4Å: Chain K: S.216, S.217, Y.221, L.222, L.225, F.286, L.293 Ligands: 3PE.17, 3PE.21, LFA.22 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:Y.221, K:L.222, K:L.225, K:F.286, K:F.286, K:L.293 Hydrogen bonds: K:S.216, K:S.217, K:V.219 3PE.21: 15 residues within 4Å: Chain K: V.184, I.187, V.195, M.215, S.216, V.219, L.222, G.226, I.229 Chain L: W.408, G.412, V.415 Ligands: 3PE.17, 3PE.20, LFA.22 16 PLIP interactions: 8 interactions with chain K, 8 interactions with chain L Hydrophobic interactions: K:V.184, K:V.184, K:I.187, K:V.219, K:L.222, K:I.229, L:W.408, L:W.408, L:W.408, L:W.408, L:W.408, L:W.408, L:V.415 Hydrogen bonds: K:S.216, K:S.216 Salt bridges: L:H.406 3PE.23: 14 residues within 4Å: Chain L: N.46, L.49, W.53, G.56, G.59, M.74, L.75, L.79, L.82, F.335, L.463, L.474, I.477, L.480 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:L.49, L:M.74, L:L.79, L:L.82, L:F.335, L:F.335, L:L.463, L:L.474, L:I.477

3 x LFA: EICOSANE(Non-covalent)

LFA.14: 10 residues within 4Å: Chain H: I.21, V.24, V.25, C.28, V.103, S.104, W.107, F.268, T.275, M.279 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:I.21, H:V.25, H:W.107, H:F.268, H:T.275 LFA.19: 7 residues within 4Å: Chain K: V.92, L.474, L.477, L.478, Y.481, I.485 Ligands: 3PE.16 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:V.92, K:L.474, K:L.477, K:L.477, K:L.478, K:Y.481, K:I.485 LFA.22: 7 residues within 4Å: Chain L: F.278, W.408, W.409, G.412, V.416 Ligands: 3PE.20, 3PE.21 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:F.278, L:W.409, L:V.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kravchuk, V. et al., A universal coupling mechanism of respiratory complex I. Nature (2022)

Release Date

2022-09-21

Peptides

NADH-quinone oxidoreductase subunit F: A
NADH dehydrogenase I subunit E: B
NADH-quinone oxidoreductase: C
NADH-quinone oxidoreductase subunit C/D: D
NADH-quinone oxidoreductase subunit B: E
NADH-quinone oxidoreductase subunit I: F
NADH-quinone oxidoreductase subunit J: G
NADH-quinone oxidoreductase subunit H: H
NADH-quinone oxidoreductase subunit A: I
NADH dehydrogenase subunit L: J
NADH dehydrogenase I subunit M: K
NADH-quinone oxidoreductase subunit N: L
NADH-quinone oxidoreductase subunit K: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
E

C
G

D
C

E
B

F
I

G
J

H
H

I
A

J
L

K
M

L
N

M
K

Membrane

We predict this structure to be a membrane protein.
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NADH-quinone oxidoreductase subunit F

NADH dehydrogenase I subunit E

NADH-quinone oxidoreductase

NADH-quinone oxidoreductase subunit C/D

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit J

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit A

NADH dehydrogenase subunit L

NADH dehydrogenase I subunit M

NADH-quinone oxidoreductase subunit N

NADH-quinone oxidoreductase subunit K

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