SMTL ID : 7z83.1

Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, 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: 13 residues within 4Å: Chain C: H.99, D.102, C.103, C.106, E.108, G.109, C.112, L.114, Q.115, R.150, T.203, G.204 Chain D: I.516 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: 10 residues within 4Å: Chain C: C.228, Q.230, C.231, I.233, G.234, C.235, 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: 15 residues within 4Å: Chain D: R.254, R.274, H.359 Chain E: S.62, C.63, C.64, G.100, T.101, G.127, 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: 13 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 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: 20 residues within 4Å: Chain A: G.61, R.62, G.63, K.72, N.90, D.92, E.93, M.94, Y.178, I.179, 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:I.179, 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:T.221 Salt bridges: A:K.72

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

NAI.3: 19 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.182, E.183, K.200, F.203, R.320, G.322, T.323, A.399 Ligands: FMN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.95 Hydrogen bonds: A:K.72, A:M.94, A:E.95, A:E.182, A:E.182, A:E.183, 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

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

3PE.13: 25 residues within 4Å: Chain D: T.402, I.403, G.406 Chain F: E.5, L.6, G.9, F.10, Q.13, V.14 Chain G: F.196, A.200, I.201, V.204, F.212, I.248, M.252, F.278, M.281, F.282, I.285, L.289, P.292, Q.296, V.297, F.300 20 PLIP interactions: 14 interactions with chain G, 5 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: G:F.196, G:A.200, G:I.201, G:V.204, G:F.212, G:I.248, G:M.252, G:F.278, G:F.278, G:F.282, G:I.285, G:I.285, G:L.289, G:F.300, F:L.6, F:F.10, F:F.10, F:Q.13, F:V.14 Hydrogen bonds: D:T.402 3PE.15: 23 residues within 4Å: Chain I: L.12, A.19, R.22, R.115, Y.119, L.122, S.126, L.141, G.145, L.148 Chain J: W.378, K.382, W.383, A.386, L.389, F.390, M.398, P.399, V.472, V.476, L.477, F.480 Ligands: 3PE.17 16 PLIP interactions: 9 interactions with chain J, 7 interactions with chain I Hydrophobic interactions: J:W.383, J:A.386, J:L.389, J:F.390, J:V.476, J:L.477, J:L.477, J:F.480, I:L.12, I:L.12, I:R.22, I:Y.119, I:L.122, I:L.141, I:L.148 Hydrogen bonds: J:W.378 3PE.16: 16 residues within 4Å: Chain I: M.168, K.169, V.172, V.173, V.176, P.234, Y.545, F.549, V.550, F.553, L.554 Chain J: F.306, F.431, V.434, A.438, R.442 16 PLIP interactions: 12 interactions with chain I, 4 interactions with chain J Hydrophobic interactions: I:M.168, I:K.169, I:K.169, I:V.173, I:V.176, I:P.234, I:Y.545, I:Y.545, I:F.549, I:F.549, I:V.550, I:F.553, J:F.306, J:V.434, J:V.434 Salt bridges: J:R.442 3PE.17: 14 residues within 4Å: Chain I: I.8, L.12, F.15, V.16, L.64, W.65, T.66, F.77, V.129 Chain J: L.477, F.480, Y.481 Ligands: 3PE.15, LFA.19 13 PLIP interactions: 8 interactions with chain I, 5 interactions with chain J Hydrophobic interactions: I:I.8, I:L.12, I:F.15, I:V.16, I:W.65, I:F.77, I:F.77, I:V.129, J:L.477, J:F.480, J:F.480 Hydrogen bonds: J:Y.481, J:Y.481 3PE.18: 20 residues within 4Å: Chain I: M.569, P.572, A.573, S.576, R.577 Chain J: T.169, K.173, I.176, Y.177, A.180, S.181, I.229, L.240 Chain K: L.289, V.416, A.419, I.420, Y.423 Ligands: 3PE.20, 3PE.21 16 PLIP interactions: 9 interactions with chain J, 4 interactions with chain I, 3 interactions with chain K Hydrophobic interactions: J:K.173, J:I.176, J:Y.177, J:Y.177, J:A.180, J:I.229, J:I.229, J:L.240, I:P.572, I:A.573, K:V.416, K:Y.423, K:Y.423 Hydrogen bonds: J:T.169 Salt bridges: I:R.577, I:R.577 3PE.20: 11 residues within 4Å: Chain J: S.216, S.217, L.222, L.225, I.229, L.240, F.286, L.293 Ligands: 3PE.18, 3PE.21, LFA.23 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:L.222, J:L.225, J:L.225, J:L.240, J:F.286, J:L.293 Hydrogen bonds: J:S.216, J:S.217 3PE.21: 17 residues within 4Å: Chain J: V.184, I.187, A.191, V.195, S.216, V.219, L.222, L.223, L.225, G.226 Chain K: H.406, W.408, G.412, V.415 Ligands: 3PE.18, 3PE.20, LFA.23 13 PLIP interactions: 7 interactions with chain J, 6 interactions with chain K Hydrophobic interactions: J:V.184, J:V.184, J:I.187, J:L.222, J:L.223, J:L.225, K:W.408, K:W.408, K:W.408, K:W.408, K:V.415 Hydrogen bonds: J:S.216 Salt bridges: K:H.406 3PE.24: 11 residues within 4Å: Chain H: H.13 Chain M: M.1, A.4, I.7, I.11, L.37, A.38, G.41, F.44, S.45 Ligands: 3PE.25 7 PLIP interactions: 6 interactions with chain M, 1 interactions with chain H Hydrophobic interactions: M:A.4, M:I.7, M:I.11, M:L.37, M:F.44 Hydrogen bonds: M:M.1 Salt bridges: H:H.13 3PE.25: 18 residues within 4Å: Chain G: I.89, D.111, L.112, N.113, I.114, F.118, M.122, L.125 Chain H: H.13, F.16, A.17, L.20, I.24 Chain M: I.33, L.37, F.44, Y.49 Ligands: 3PE.24 17 PLIP interactions: 7 interactions with chain G, 5 interactions with chain M, 5 interactions with chain H Hydrophobic interactions: G:I.89, G:L.112, G:I.114, G:F.118, G:F.118, G:L.125, M:I.33, M:L.37, M:F.44, M:F.44, H:F.16, H:A.17, H:I.24 Hydrogen bonds: G:N.113, M:Y.49 Salt bridges: H:H.13, H:H.13

4 x LFA: EICOSANE(Non-covalent)

LFA.14: 6 residues within 4Å: Chain G: I.21, V.24, C.28, V.103, W.107, F.268 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:V.24, G:V.103, G:W.107, G:W.107, G:F.268, G:F.268 LFA.19: 8 residues within 4Å: Chain J: I.346, L.474, L.477, L.478, Y.481, P.484, I.485 Ligands: 3PE.17 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:I.346, J:L.474, J:L.477, J:L.478, J:Y.481, J:P.484 LFA.22: 10 residues within 4Å: Chain J: Y.112, F.115, W.157 Chain K: F.366, W.367, A.374, T.377, L.381, M.388, Y.433 12 PLIP interactions: 6 interactions with chain K, 6 interactions with chain J Hydrophobic interactions: K:F.366, K:F.366, K:A.374, K:T.377, K:L.381, K:Y.433, J:Y.112, J:Y.112, J:F.115, J:F.115, J:W.157, J:W.157 LFA.23: 7 residues within 4Å: Chain K: W.408, W.409, G.412, A.413, V.416 Ligands: 3PE.20, 3PE.21 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:W.409, K: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 CD: D
NADH-quinone oxidoreductase subunit B: E
NADH-quinone oxidoreductase subunit I: F
NADH-quinone oxidoreductase subunit H: G
NADH-quinone oxidoreductase subunit A: H
NADH-quinone oxidoreductase subunit L: I
NADH dehydrogenase I subunit M: J
NADH-quinone oxidoreductase subunit N: K
NADH-quinone oxidoreductase subunit K: L
NADH-quinone oxidoreductase subunit J: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
E

C
G

D
C

E
B

F
I

G
H

H
A

I
L

J
M

K
N

L
K

M
J

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 CD

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit A

NADH-quinone oxidoreductase subunit L

NADH dehydrogenase I subunit M

NADH-quinone oxidoreductase subunit N

NADH-quinone oxidoreductase subunit K

NADH-quinone oxidoreductase subunit J

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