SMTL ID : 7vy9.1

Membrane arm of active state CI from Q10-NADH dataset

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.1: 19 residues within 4Å: Chain A: Y.20 Chain Q: L.163, L.170, M.284, L.287, L.288, Y.291, R.295 Chain T: P.563, T.566, S.567, Q.570, M.571 Chain Y: N.144, L.147, Y.148, F.151, Y.152, A.155 14 PLIP interactions: 3 interactions with chain T, 6 interactions with chain Q, 4 interactions with chain Y, 1 interactions with chain A Hydrophobic interactions: T:P.563, T:T.566, T:Q.570, Q:L.163, Q:L.288, Q:Y.291, Q:Y.291, Y:L.147, Y:Y.148, Y:F.151, Y:Y.152 Hydrogen bonds: Q:Y.291, A:Y.20 Salt bridges: Q:R.295 PEE.4: 17 residues within 4Å: Chain B: A.39 Chain E: F.109, I.110, W.111, Y.112, T.113 Chain R: I.3 Chain U: G.42, L.45, N.46, S.50, F.57 Chain Z: M.98, N.99, F.104, M.108 Ligands: CDL.24 8 PLIP interactions: 4 interactions with chain U, 3 interactions with chain Z, 1 interactions with chain E Hydrophobic interactions: U:L.45, U:F.57, Z:F.104 Hydrogen bonds: U:S.50, U:S.50, Z:N.99, Z:L.100, E:F.109 PEE.10: 16 residues within 4Å: Chain C: F.7, L.8, A.11, E.15, L.18, F.22, G.25, G.26 Chain R: A.99, A.103, W.106, T.107 Chain Z: K.291, P.295, A.299, M.302 14 PLIP interactions: 2 interactions with chain Z, 8 interactions with chain C, 4 interactions with chain R Hydrophobic interactions: Z:A.299, C:F.7, C:L.8, C:A.11, C:L.18, C:L.18, C:F.22, C:F.22, C:F.22, R:A.103, R:W.106, R:W.106 Salt bridges: Z:K.291 Hydrogen bonds: R:W.106 PEE.14: 8 residues within 4Å: Chain D: I.109, A.112, A.113, Y.116, T.120 Chain T: F.568, I.569, K.572 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain T Hydrophobic interactions: D:I.109, D:A.112, D:Y.116, D:Y.116, T:F.568, T:I.569 Salt bridges: T:K.572 PEE.17: 20 residues within 4Å: Chain K: Q.54, N.85, R.86 Chain T: T.166, Q.170, L.173, Y.174, I.177, I.180, G.228, L.229, L.280, Y.529, M.533, H.534, T.538, N.541 Chain Y: M.398, M.401, L.405 15 PLIP interactions: 11 interactions with chain T, 2 interactions with chain Y, 2 interactions with chain K Hydrophobic interactions: T:L.173, T:L.173, T:I.177, T:I.177, T:I.180, T:L.229, T:L.280, T:H.534, Y:L.405, Y:L.405, K:R.86 Hydrogen bonds: T:Q.170, K:Q.54 Salt bridges: T:H.534, T:H.534 PEE.18: 15 residues within 4Å: Chain J: I.80, Y.84, H.88, K.92 Chain T: W.66, H.67, W.68, L.78, N.136, F.138 Chain Y: P.371, L.449 Ligands: CDL.6, CDL.15, PLX.22 15 PLIP interactions: 2 interactions with chain Y, 9 interactions with chain T, 4 interactions with chain J Hydrophobic interactions: Y:P.371, Y:L.449, T:W.66, T:W.66, T:W.66, T:W.66, T:L.78, T:L.78, T:F.138, J:Y.84, J:Y.84 Hydrogen bonds: T:H.67, T:H.67 Salt bridges: J:H.88, J:K.92 PEE.20: 18 residues within 4Å: Chain D: L.123, E.130, W.132 Chain Q: E.274, I.276, I.277 Chain Y: Y.152, A.155, P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201, V.205 Ligands: PLX.21 7 PLIP interactions: 5 interactions with chain Y, 1 interactions with chain Q, 1 interactions with chain D Hydrophobic interactions: Y:P.159, Y:F.194, Y:L.197, Y:V.205, Q:I.276, D:W.132 Hydrogen bonds: Y:S.191 PEE.23: 12 residues within 4Å: Chain R: V.11, S.15, V.18, L.19, F.22, W.23, L.27 Chain Z: R.62, I.76, L.77 Ligands: PLX.11, CDL.24 6 PLIP interactions: 3 interactions with chain R, 3 interactions with chain Z Hydrophobic interactions: R:V.11, R:V.18, R:L.19, Z:I.76, Z:L.77 Salt bridges: Z:R.62 PEE.25: 18 residues within 4Å: Chain C: V.17, I.24 Chain E: I.9, L.12, Y.16 Chain Z: P.180, A.182, M.183, F.186, I.187, I.273, Y.277, F.280, L.288, S.292, F.293, L.296, W.303 11 PLIP interactions: 9 interactions with chain Z, 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: Z:P.180, Z:A.182, Z:M.183, Z:F.186, Z:F.186, Z:Y.277, Z:F.280, Z:L.296, Z:W.303, C:I.24, E:L.12

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 26 residues within 4Å: Chain D: I.27, A.30, T.31, I.34, V.35, Y.38, S.39, L.42, K.43, Y.58, S.62, I.65, G.66, F.69 Chain Q: P.110, F.113, L.153, M.157, L.160, I.164 Chain T: M.576, V.577, Q.580, T.594, I.597, S.598 20 PLIP interactions: 11 interactions with chain D, 5 interactions with chain Q, 4 interactions with chain T Hydrophobic interactions: D:I.27, D:A.30, D:T.31, D:I.34, D:Y.38, D:Y.38, D:L.42, D:Y.58, D:I.65, D:F.69, Q:P.110, Q:F.113, Q:L.153, Q:L.160, Q:I.164, T:V.577, T:T.594, T:I.597 Salt bridges: D:K.43 Hydrogen bonds: T:Q.580 CDL.3: 15 residues within 4Å: Chain D: Y.107, G.108, C.114 Chain T: W.557 Chain W: P.81, T.82, P.83, S.86, L.87, G.89, A.90, G.93, I.94, L.97 Chain Y: L.264 13 PLIP interactions: 5 interactions with chain W, 4 interactions with chain T, 3 interactions with chain D, 1 interactions with chain Y Hydrophobic interactions: W:P.83, W:L.87, W:A.90, W:I.94, W:L.97, T:W.557, T:W.557, T:W.557, T:W.557, D:Y.107, Y:L.264 Hydrogen bonds: D:Y.107, D:Y.107 CDL.6: 30 residues within 4Å: Chain I: I.24, L.25, G.28, V.31, I.35, T.36, N.39, V.40, E.44, H.64 Chain J: Y.83, Y.84, H.88 Chain L: P.43, L.46, A.47, R.48, H.55 Chain M: V.50, S.53, Y.58 Chain T: T.13, T.16, M.20, N.65, F.80 Chain Y: L.446 Ligands: CDL.15, PEE.18, PLX.22 19 PLIP interactions: 4 interactions with chain L, 3 interactions with chain M, 8 interactions with chain I, 1 interactions with chain T, 3 interactions with chain J Hydrophobic interactions: L:P.43, L:L.46, L:A.47, M:V.50, M:V.50, I:I.24, I:I.24, I:L.25, I:V.31, I:I.35, T:F.80, J:Y.83, J:Y.84 Hydrogen bonds: L:R.48, M:Y.58, I:N.39, I:N.39 Salt bridges: I:H.64, J:H.88 CDL.9: 33 residues within 4Å: Chain 2: K.303, Y.304 Chain O: F.37, Y.40, C.41, I.45, A.48, P.53, V.54, V.55 Chain Q: P.238, V.239, S.242, L.243, M.245, V.246, L.335 Chain V: W.10 Chain Y: P.13, W.16, M.17, T.90, R.91, L.94, T.97, M.98, L.101, L.104, F.105, V.127, I.131, R.135 Ligands: CDL.19 20 PLIP interactions: 10 interactions with chain Y, 3 interactions with chain O, 3 interactions with chain Q, 1 interactions with chain V, 3 interactions with chain 2 Hydrophobic interactions: Y:P.13, Y:W.16, Y:W.16, Y:T.97, Y:L.101, Y:L.104, Y:F.105, Y:V.127, Y:I.131, O:I.45, O:A.48, Q:L.243, Q:V.246, Q:L.335, V:W.10 Hydrogen bonds: Y:R.91, O:V.54, 2:Y.304, 2:Y.304 Salt bridges: 2:K.303 CDL.13: 26 residues within 4Å: Chain D: L.33, A.37, I.40, P.45, A.46, S.47, F.48, G.51, V.52, T.55 Chain S: A.13, I.14, L.16, A.17, M.21, Y.22, R.23 Chain T: K.585, L.589, I.593, M.596 Chain U: S.21, K.23, T.88, S.95, M.99 15 PLIP interactions: 2 interactions with chain U, 4 interactions with chain T, 5 interactions with chain D, 4 interactions with chain S Hydrogen bonds: U:T.88 Salt bridges: U:K.23, T:K.585, S:R.23 Hydrophobic interactions: T:L.589, T:L.589, T:I.593, D:L.33, D:L.33, D:I.40, D:F.48, D:T.55, S:I.14, S:L.16, S:M.21 CDL.15: 31 residues within 4Å: Chain I: L.17 Chain T: I.19, M.20, N.23, Y.27, L.78, R.116, K.119, Y.120, L.123, I.126, I.130, G.146, M.150, L.153 Chain Y: P.353, L.354, T.357, W.358, V.361, T.365, L.369, P.370, P.371, S.372, L.445, T.448, L.449 Ligands: CDL.6, PEE.18, PLX.22 23 PLIP interactions: 13 interactions with chain T, 10 interactions with chain Y Hydrophobic interactions: T:I.19, T:L.78, T:L.123, T:L.123, T:I.126, T:I.130, T:L.153, Y:W.358, Y:V.361, Y:L.369, Y:P.371, Y:L.445, Y:L.445, Y:T.448, Y:L.449 Hydrogen bonds: T:Y.120, Y:P.353, Y:T.357 Salt bridges: T:R.116, T:K.119, T:K.119, T:K.119, T:K.119 CDL.16: 17 residues within 4Å: Chain K: G.105, F.106, F.109, M.110 Chain T: L.290, I.293, T.294, L.410, S.417, A.421, R.425, L.500, L.504, S.517, T.519, Y.520, S.523 16 PLIP interactions: 2 interactions with chain K, 14 interactions with chain T Hydrophobic interactions: K:F.106, K:F.109, T:L.290, T:I.293, T:L.410, T:A.421, T:L.500, T:L.504, T:T.519 Hydrogen bonds: T:S.517, T:S.517, T:T.519, T:Y.520, T:Y.520, T:S.523 Salt bridges: T:R.425 CDL.19: 20 residues within 4Å: Chain 0: F.168, W.169, T.170, M.171 Chain O: T.28, P.30, R.31, V.33, Y.34 Chain Q: P.256, P.338 Chain V: F.21, L.25, R.28, S.29, K.32 Chain Y: F.105, L.117, L.121 Ligands: CDL.9 12 PLIP interactions: 3 interactions with chain V, 3 interactions with chain 0, 3 interactions with chain Y, 1 interactions with chain Q, 2 interactions with chain O Hydrogen bonds: V:L.25, 0:T.170, 0:T.170 Salt bridges: V:R.28, V:K.32 Hydrophobic interactions: 0:F.168, Y:F.105, Y:L.117, Y:L.121, Q:P.256, O:Y.34, O:Y.34 CDL.24: 16 residues within 4Å: Chain U: I.15, G.16, Y.28, L.31, G.32, V.35, V.82, W.83, V.84, F.93 Chain Z: S.67, I.68, S.69, I.73 Ligands: PEE.4, PEE.23 17 PLIP interactions: 5 interactions with chain Z, 12 interactions with chain U Hydrophobic interactions: Z:I.68, Z:I.73, U:I.15, U:L.31, U:V.35, U:W.83, U:W.83, U:W.83, U:W.83, U:V.84, U:F.93, U:F.93 Hydrogen bonds: Z:I.68, Z:S.69, Z:S.69, U:W.83, U:V.84

1 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Covalent)

8Q1.5: 19 residues within 4Å: Chain F: S.44, L.45 Chain T: F.513, Y.515 Chain X: H.11, Q.12, L.16, W.29, M.43, R.46, F.47, H.50, K.51, A.59, L.62, A.66, E.69, F.70, G.73 11 PLIP interactions: 2 interactions with chain F, 8 interactions with chain X, 1 interactions with chain T Hydrogen bonds: F:S.44, F:L.45, X:H.11, X:H.50, X:A.59 Hydrophobic interactions: X:F.47, X:K.51, X:A.59, X:E.69, X:F.70, T:F.513

6 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.7: 11 residues within 4Å: Chain I: I.66, R.72, T.73, F.74, Y.75, D.76 Chain M: F.43, F.55 Chain V: C.23 Chain Y: L.36, S.40 9 PLIP interactions: 3 interactions with chain M, 3 interactions with chain I, 3 interactions with chain Y Hydrophobic interactions: M:F.43, M:F.43, M:F.55, I:I.66, I:F.74, Y:L.36 Salt bridges: I:D.76 Hydrogen bonds: Y:S.40, Y:S.40 PLX.8: 21 residues within 4Å: Chain O: R.9, P.11, L.12, F.14, F.72, L.76, R.79 Chain P: P.1, F.2, F.3 Chain Q: I.202, L.203, I.207, T.210, L.332, V.336, M.339, A.342, L.343, S.345, L.346 14 PLIP interactions: 7 interactions with chain Q, 7 interactions with chain O Hydrophobic interactions: Q:L.203, Q:I.207, Q:L.332, Q:L.332, Q:V.336, Q:V.336, Q:A.342, O:F.72, O:F.72, O:L.76, O:L.76 Hydrogen bonds: O:L.12 Salt bridges: O:R.9, O:R.79 PLX.11: 8 residues within 4Å: Chain R: L.13, L.16, L.17, I.20, W.23, L.24, P.25 Ligands: PEE.23 6 PLIP interactions: 6 interactions with chain R Hydrophobic interactions: R:L.13, R:L.16, R:L.16, R:L.17, R:I.20, R:L.24 PLX.12: 11 residues within 4Å: Chain P: L.13 Chain R: N.83, T.86, M.90, F.93 Chain U: S.148, Y.149, T.151, W.152, I.155, W.159 11 PLIP interactions: 5 interactions with chain U, 1 interactions with chain P, 5 interactions with chain R Hydrophobic interactions: U:T.151, U:W.152, U:I.155, U:W.159, P:L.13, R:F.93, R:F.93 pi-Cation interactions: U:Y.149 Hydrogen bonds: R:N.83, R:T.86, R:T.86 PLX.21: 16 residues within 4Å: Chain D: D.85, L.87, F.90, L.119, A.122 Chain Y: N.188, S.189, W.190, I.193, M.201, G.211, L.212, M.257, F.261, L.264 Ligands: PEE.20 10 PLIP interactions: 6 interactions with chain Y, 4 interactions with chain D Hydrophobic interactions: Y:W.190, Y:W.190, Y:I.193, Y:L.212, Y:F.261, D:F.90, D:L.119, D:L.119, D:A.122 pi-Cation interactions: Y:W.190 PLX.22: 20 residues within 4Å: Chain I: H.64 Chain M: S.53, V.56, A.57, Y.58 Chain T: I.19, M.20, N.23, W.66 Chain Y: L.39, P.64, V.67, W.71, P.443, L.446, L.447, N.450 Ligands: CDL.6, CDL.15, PEE.18 10 PLIP interactions: 8 interactions with chain Y, 1 interactions with chain T, 1 interactions with chain M Hydrophobic interactions: Y:L.39, Y:V.67, Y:W.71, Y:P.443, Y:L.446, Y:L.447, Y:N.450, T:N.23, M:V.56 Hydrogen bonds: Y:N.450

1 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)

UQ.26: 9 residues within 4Å: Chain Z: I.11, L.14, A.18, R.25, D.51, A.52, L.55, F.224, M.225 10 PLIP interactions: 10 interactions with chain Z Hydrophobic interactions: Z:I.11, Z:L.14, Z:L.14, Z:A.18, Z:D.51, Z:A.52, Z:L.55, Z:F.224, Z:F.224 pi-Cation interactions: Z:R.274

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.27: 16 residues within 4Å: Chain 2: I.31, C.32, S.33, K.35, E.53, L.79, Y.83, Q.97, L.100, R.104, R.126, D.131, F.134, M.138, E.191, Y.198 12 PLIP interactions: 12 interactions with chain 2 Hydrogen bonds: 2:C.32, 2:Y.83, 2:Q.97, 2:Q.97, 2:R.104, 2:R.104, 2:E.191 Salt bridges: 2:K.35, 2:K.35, 2:R.126 pi-Stacking: 2:F.134, 2:F.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, J. et al., The coupling mechanism of mammalian mitochondrial complex I. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-12-14

Peptides

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: A
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: B
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: E
Acyl carrier protein: F
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: G
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: H
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: I
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: J
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: K
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: L
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: M
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: N
NADH dehydrogenase [ubiquinone] 1 subunit C2: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: P
NADH-ubiquinone oxidoreductase chain 2: Q
NADH-ubiquinone oxidoreductase chain 3: R
NADH-ubiquinone oxidoreductase chain 4L: S
NADH-ubiquinone oxidoreductase chain 5: T
NADH-ubiquinone oxidoreductase chain 6: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: X
NADH-ubiquinone oxidoreductase chain 4: Y
NADH-ubiquinone oxidoreductase chain 1: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: 0
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: 1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
S

C
U

D
V

E
W

F
X

G
Y

H
Z

I
a

J
b

K
c

L
d

M
e

N
f

O
g

P
h

Q
i

R
j

S
k

T
l

U
m

V
n

W
o

X
p

Y
r

Z
s

0
u

1
v

2
w

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH-ubiquinone oxidoreductase chain 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

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