SMTL ID : 7zci.1

Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting 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: 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 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: 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: 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: 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 18 PLIP interactions: 18 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:E.93, A:M.94, A:G.181, A:E.182, A:E.182, 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: 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 11 PLIP interactions: 11 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 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: 10 residues within 4Å: Chain C: Y.32, 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 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.617, C:E.647, C:D.731

5 x LFA: EICOSANE(Non-covalent)

LFA.13: 8 residues within 4Å: Chain G: I.21, V.24, C.28, S.104, W.107, F.268, I.269, T.275 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:I.21, G:V.24, G:F.268, G:F.268, G:I.269, G:T.275 LFA.15: 6 residues within 4Å: Chain H: V.101, I.105 Chain K: L.15 Chain M: L.139, E.142, M.146 5 PLIP interactions: 3 interactions with chain M, 1 interactions with chain H, 1 interactions with chain K Hydrophobic interactions: M:L.139, M:E.142, M:E.142, H:V.101, K:L.15 LFA.20: 10 residues within 4Å: Chain I: G.39, L.43, T.87, S.90, G.94, F.97, M.336, F.340, I.471, P.474 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:L.43, I:F.97, I:F.97, I:F.97, I:F.340, I:F.340 LFA.25: 10 residues within 4Å: Chain J: Y.112, F.115, W.122, W.157 Chain K: F.366, W.367, T.377, V.378, L.381, Y.433 14 PLIP interactions: 7 interactions with chain K, 7 interactions with chain J Hydrophobic interactions: K:F.366, K:F.366, K:T.377, K:V.378, K:L.381, K:Y.433, K:Y.433, J:Y.112, J:F.115, J:F.115, J:F.115, J:W.122, J:W.157, J:W.157 LFA.27: 7 residues within 4Å: Chain K: F.278, I.282, W.408, W.409, G.412 Ligands: 3PE.23, 3PE.24 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:F.278, K:I.282, K:I.282, K:W.408, K:W.409, K:W.409

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

3PE.14: 15 residues within 4Å: Chain G: 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: F.44, Y.49 Ligands: 3PE.28 9 PLIP interactions: 4 interactions with chain H, 3 interactions with chain G, 2 interactions with chain M Hydrophobic interactions: H:F.16, H:A.17, H:I.24, G:L.112, G:I.114, M:F.44 Salt bridges: H:H.13 Hydrogen bonds: G:N.113, M:Y.49 3PE.16: 24 residues within 4Å: Chain I: L.12, A.19, R.22, G.23, R.115, Y.119, S.126, 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.19 17 PLIP interactions: 6 interactions with chain I, 11 interactions with chain J Hydrophobic interactions: I:L.12, I:L.12, I:L.141, I:L.141, I:L.148, J:W.383, J:A.386, J:L.389, 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 3PE.17: 16 residues within 4Å: Chain I: A.165, M.168, K.169, V.172, V.176, L.235, Y.545, F.549, V.550, F.553, L.554 Chain J: F.306, F.427, V.434, R.442 Ligands: 3PE.21 12 PLIP interactions: 4 interactions with chain J, 8 interactions with chain I Hydrophobic interactions: J:F.427, J:V.434, J:V.434, I:V.172, I:V.176, I:Y.545, I:Y.545, I:F.549, I:F.549, I:V.550, I:F.553 Salt bridges: J:R.442 3PE.18: 12 residues within 4Å: Chain I: L.299, F.363, L.427, R.431, L.511, W.512, V.519, T.520, I.522, G.528, W.535, W.539 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:L.299, I:L.427, I:L.511, I:W.512, I:I.522, I:W.535, I:W.535, I:W.539 Salt bridges: I:R.431 3PE.19: 16 residues within 4Å: Chain I: I.8, I.9, L.12, I.13, V.16, L.64, W.65, T.66, F.77, V.129, L.141 Chain J: V.476, L.477, F.480, Y.481 Ligands: 3PE.16 19 PLIP interactions: 13 interactions with chain I, 6 interactions with chain J Hydrophobic interactions: I:I.8, I:I.9, I:L.12, I:I.13, I:W.65, I:W.65, I:W.65, I:W.65, I:F.77, I:F.77, I:V.129, I:L.141, J:V.476, J:F.480, J:F.480, J:Y.481 Hydrogen bonds: I:T.66, J:Y.481, J:Y.481 3PE.21: 17 residues within 4Å: Chain I: F.180, I.187, M.214, L.220, M.221, G.224, L.233, P.234, V.286 Chain J: F.299, F.415, P.419, V.420, V.423, F.427, F.431 Ligands: 3PE.17 11 PLIP interactions: 8 interactions with chain J, 3 interactions with chain I Hydrophobic interactions: J:F.299, J:F.299, J:V.420, J:V.420, J:V.423, J:F.427, J:F.427, J:F.431, I:F.180, I:L.220, I:V.286 3PE.22: 17 residues within 4Å: Chain I: M.569, A.573, S.576, R.577 Chain J: K.165, T.169, K.173, I.176, Y.177, A.180, I.229, V.233 Chain K: L.289, A.419, I.420, Y.423 Ligands: 3PE.23 17 PLIP interactions: 7 interactions with chain J, 6 interactions with chain K, 4 interactions with chain I Hydrophobic interactions: J:I.176, J:Y.177, J:A.180, J:I.229, J:I.229, J:V.233, K:L.289, K:A.419, K:Y.423, K:Y.423, K:Y.423, I:A.573, I:R.577 Salt bridges: J:K.165, I:R.577, I:R.577 Hydrogen bonds: K:Y.423 3PE.23: 12 residues within 4Å: Chain J: S.216, G.218, Y.221, L.222, L.225, F.228, I.229, L.240 Chain K: V.416 Ligands: 3PE.22, 3PE.24, LFA.27 9 PLIP interactions: 8 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:Y.221, J:L.222, J:L.225, J:F.228, J:I.229, J:L.240, K:V.416 Hydrogen bonds: J:S.216, J:G.218 3PE.24: 15 residues within 4Å: Chain J: V.184, A.191, V.195, V.219, L.222, L.223, L.225, G.226, I.229 Chain K: H.406, W.408, V.411, G.412 Ligands: 3PE.23, LFA.27 15 PLIP interactions: 11 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: J:V.184, J:V.184, J:A.191, J:V.195, J:V.219, J:L.222, J:L.222, J:L.222, J:L.223, J:L.225, J:I.229, K:W.408, K:W.408, K:V.411 Salt bridges: K:H.406 3PE.26: 16 residues within 4Å: Chain K: L.49, W.53, G.56, Q.57, A.58, G.71, L.75, G.78, L.79, L.82, F.335, I.459, L.463, L.467, L.480, A.481 13 PLIP interactions: 13 interactions with chain K Hydrophobic interactions: K:L.49, K:W.53, K:W.53, K:L.79, K:L.82, K:L.82, K:F.335, K:F.335, K:I.459, K:L.463, K:L.467, K:L.480, K:A.481 3PE.28: 13 residues within 4Å: Chain H: H.13 Chain M: M.1, F.3, A.4, I.7, C.8, I.11, L.37, A.38, G.41, F.44, S.45 Ligands: 3PE.14 9 PLIP interactions: 6 interactions with chain M, 3 interactions with chain H Hydrophobic interactions: M:F.3, M:A.4, M:I.7, M:I.11, M:L.37 Hydrogen bonds: M:M.1, H:T.5, H:T.5 Salt bridges: H:H.13

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.
Show / Hide

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

Related Entries With Identical Sequence