SMTL ID : 7z7v.1

Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready 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)(Covalent)

SF4.1: 13 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, A.401 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.512 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.102 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: 15 residues within 4Å: Chain D: R.250, R.270, H.355 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: 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: 15 residues within 4Å: Chain F: L.50, C.60, V.61, A.62, C.63, N.64, L.65, C.66, L.77, F.92, C.109, P.110, T.111, A.113, 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 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.178, A:I.179, A:E.182, 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:G.181, A:E.183, A:N.217, A:N.218, A:N.218, A:T.221 Water bridges: A:G.61, A:G.61, A:K.72, A:G.181 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, F.203, R.320, G.322, T.323, A.399 Ligands: FMN.2 16 PLIP interactions: 16 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 Water bridges: A:E.93, A:E.182, A:N.218, A:A.399 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: 11 residues within 4Å: Chain C: Y.32, F.33, C.34, W.35, G.43, A.44, C.45, R.46, 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 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.617, C:E.647, C:D.731, H2O.8, H2O.18

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

3PE.13: 16 residues within 4Å: Chain D: Q.396, K.401 Chain F: L.7, V.8, F.10, G.11, T.12, R.15 Chain G: V.189, F.193, I.197, F.257, F.300, I.304, L.308 Ligands: 3PE.14 16 PLIP interactions: 7 interactions with chain G, 7 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: G:V.189, G:F.193, G:I.197, G:F.257, G:F.300, G:I.304, G:L.308, F:F.10, F:F.10, F:F.10, F:F.10, F:R.15 Salt bridges: F:R.15, F:R.15 Hydrogen bonds: D:Q.396, D:K.401 3PE.14: 25 residues within 4Å: Chain D: T.398, I.399, G.402, Q.405 Chain F: M.1, G.9, F.10, Q.13, V.14, I.17 Chain G: A.200, I.201, P.211, F.212, M.252, F.278, M.281, F.282, I.285, L.289, P.292, Q.296, V.297, F.300 Ligands: 3PE.13 18 PLIP interactions: 10 interactions with chain G, 6 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: G:A.200, G:F.212, G:F.212, G:F.278, G:F.282, G:I.285, G:L.289, G:P.292, G:F.300, G:F.300, F:F.10, F:F.10, F:Q.13, F:Q.13, F:V.14, F:I.17 Hydrogen bonds: D:T.398, D:Q.405 3PE.16: 15 residues within 4Å: Chain G: D.111, L.112, N.113, I.114, F.118, L.125 Chain H: H.13, F.16, A.17, L.20, I.24 Chain M: L.37, F.44, Y.49 Ligands: 3PE.28 15 PLIP interactions: 6 interactions with chain G, 5 interactions with chain H, 4 interactions with chain M Hydrophobic interactions: G:L.112, G:I.114, G:F.118, G:L.125, H:F.16, H:F.16, H:A.17, M:L.37, M:F.44, M:F.44 Hydrogen bonds: G:N.113, M:Y.49 Water bridges: G:I.114 Salt bridges: H:H.13, H:H.13 3PE.17: 8 residues within 4Å: Chain G: K.303, P.307, I.311 Chain H: F.108, L.111, V.115, V.118, R.119 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:F.108, H:L.111, H:L.111, G:P.307, G:I.311 Salt bridges: H:R.119 3PE.18: 27 residues within 4Å: Chain I: I.8, L.12, A.19, R.22, G.23, R.115, Y.119, L.122, S.126, V.129, L.141, G.145, L.148 Chain J: W.378, M.381, K.382, W.383, A.386, L.389, F.390, M.398, P.399, V.472, V.476, L.477, F.480 Ligands: 3PE.20 22 PLIP interactions: 12 interactions with chain I, 10 interactions with chain J Hydrophobic interactions: I:I.8, I:L.12, I:L.12, I:L.122, I:V.129, I:L.141, I:L.148, J:W.383, J:A.386, J:L.389, J:F.390, J:V.472, J:V.476, J:L.477, J:L.477, J:F.480 Hydrogen bonds: I:R.22, J:W.378 Water bridges: I:R.22, I:R.22, I:R.115 Salt bridges: I:R.115 3PE.20: 14 residues within 4Å: Chain I: A.5, I.8, I.9, L.12, I.13, V.16, L.64, W.65, T.66 Chain J: L.477, F.480, Y.481 Ligands: 3PE.18, LFA.23 19 PLIP interactions: 11 interactions with chain I, 8 interactions with chain J Hydrophobic interactions: I:A.5, I:I.8, I:I.8, I:I.9, I:L.12, I:I.13, I:V.16, I:L.64, I:W.65, I:W.65, J:L.477, J:F.480, J:F.480, J:F.480, J:Y.481, J:Y.481 Hydrogen bonds: I:T.66, J:Y.481, J:Y.481 3PE.21: 21 residues within 4Å: Chain I: M.569, N.570, A.573, S.576, R.577 Chain J: K.165, T.169, K.173, I.176, Y.177, A.180, S.181, I.229, V.233, L.240 Chain K: L.289, V.416, A.419, Y.423 Ligands: 3PE.24, 3PE.25 16 PLIP interactions: 3 interactions with chain I, 9 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: I:A.573, J:Y.177, J:Y.177, J:Y.177, J:A.180, J:I.229, J:I.229, J:V.233, J:L.240, K:V.416, K:A.419, K:Y.423, K:Y.423 Salt bridges: I:R.577, I:R.577, J:K.165 3PE.22: 17 residues within 4Å: Chain I: A.165, M.168, K.169, V.172, V.173, F.180, P.234, L.235, Y.545, F.549, V.550, F.553, L.554 Chain J: F.306, F.427, V.434, R.442 16 PLIP interactions: 14 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: I:M.168, I:K.169, I:K.169, I:V.172, I:V.173, I:F.180, I:P.234, I:L.235, I:Y.545, I:F.549, I:F.549, I:F.549, I:F.553, I:F.553, J:V.434 Salt bridges: J:R.442 3PE.24: 10 residues within 4Å: Chain J: S.216, S.217, G.218, Y.221, L.222, L.225, L.293 Ligands: 3PE.21, 3PE.25, C14.26 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:Y.221, J:L.225, J:L.293 Hydrogen bonds: J:S.216, J:S.216 3PE.25: 19 residues within 4Å: Chain J: V.184, I.187, A.188, V.195, M.215, S.216, V.219, L.222, L.223, G.226, I.229 Chain K: W.408, V.411, G.412, V.415, V.416 Ligands: 3PE.21, 3PE.24, C14.26 19 PLIP interactions: 10 interactions with chain J, 9 interactions with chain K Hydrophobic interactions: J:V.184, J:V.184, J:I.187, J:A.188, J:V.219, J:L.222, J:L.223, J:I.229, K:W.408, K:W.408, K:W.408, K:W.408, K:W.408, K:V.411, K:V.415, K:V.416 Hydrogen bonds: J:S.216 Water bridges: J:N.198 Salt bridges: K:H.406 3PE.27: 16 residues within 4Å: Chain K: N.46, L.49, W.53, G.56, Q.57, G.59, M.74, L.75, G.78, L.79, L.82, A.331, F.335, L.474, I.477, A.481 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:M.74, K:L.75, K:L.75, K:L.79, K:L.82, K:A.331, K:F.335, K:I.477, K:A.481 Hydrogen bonds: K:Q.57 3PE.28: 13 residues within 4Å: Chain H: H.13 Chain M: M.1, F.3, A.4, I.7, I.11, I.34, L.37, A.38, G.41, F.44, S.45 Ligands: 3PE.16 9 PLIP interactions: 1 interactions with chain H, 8 interactions with chain M Salt bridges: H:H.13 Hydrophobic interactions: M:F.3, M:I.7, M:I.11, M:I.34, M:L.37, M:F.44 Hydrogen bonds: M:M.1, M:A.4

3 x LFA: EICOSANE(Non-covalent)

LFA.15: 9 residues within 4Å: Chain G: I.21, V.24, V.25, C.28, V.103, S.104, W.107, F.268, T.275 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:I.21, G:V.25, G:V.103, G:V.103, G:F.268, G:T.275 LFA.19: 4 residues within 4Å: Chain I: R.592, A.596 Chain M: G.95, L.99 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain I Hydrophobic interactions: M:L.99, I:A.596 LFA.23: 7 residues within 4Å: Chain J: V.92, L.474, L.477, L.478, Y.481, I.485 Ligands: 3PE.20 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:V.92, J:L.474, J:L.477, J:L.478, J:Y.481, J:I.485

1 x C14: TETRADECANE(Non-covalent)

C14.26: 8 residues within 4Å: Chain K: F.278, W.408, W.409, G.412, A.413, V.416 Ligands: 3PE.24, 3PE.25 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:F.278, K:W.408, 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 C/D: 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 dehydrogenase 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 C/D

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit I

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

NADH-quinone oxidoreductase subunit J

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