SMTL ID : 7vxs.1

Membrane arm of active state CI from Q10 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

10 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 27 residues within 4Å: Chain D: S.24, I.27, T.31, I.34, V.35, Y.38, S.39, L.42, K.43, R.57, Y.58, S.62, I.65, G.66, F.69 Chain Q: P.110, H.112, F.113, L.153, M.157, L.160 Chain T: M.576, Q.580, I.597, S.598, L.601, F.602 17 PLIP interactions: 9 interactions with chain D, 5 interactions with chain Q, 3 interactions with chain T Hydrophobic interactions: D:I.34, D:I.34, D:V.35, D:Y.38, D:Y.38, D:L.42, D:F.69, D:F.69, Q:P.110, Q:P.110, Q:F.113, Q:L.153, Q:L.160, T:I.597, T:L.601, T:F.602 Hydrogen bonds: D:R.57 CDL.2: 16 residues within 4Å: Chain D: Y.107, G.108, A.111, C.114 Chain T: W.557, L.558 Chain W: P.81, P.83, S.86, L.87, G.89, A.90, G.93, I.94, L.97, F.98 9 PLIP interactions: 2 interactions with chain T, 4 interactions with chain W, 3 interactions with chain D Hydrophobic interactions: T:W.557, T:W.557, W:P.83, W:I.94, W:L.97, W:F.98, D:Y.107, D:A.111 Hydrogen bonds: D:Y.107 CDL.5: 28 residues within 4Å: Chain I: I.24, L.25, V.31, A.32, I.35, T.36, N.39, V.40, E.44, H.64 Chain J: W.79, Y.83, H.88 Chain L: P.43, V.44, R.48, H.55 Chain M: V.50, S.53, Y.58 Chain T: L.9, T.13, N.65, F.80 Chain Y: L.442 Ligands: PEE.6, CDL.14, PLX.21 19 PLIP interactions: 2 interactions with chain J, 2 interactions with chain T, 8 interactions with chain I, 3 interactions with chain M, 1 interactions with chain Y, 3 interactions with chain L Hydrophobic interactions: J:W.79, T:L.9, T:F.80, I:I.24, I:L.25, I:V.31, I:A.32, I:I.35, M:V.50, M:V.50, Y:L.442, L:P.43, L:V.44 Salt bridges: J:H.88, I:H.64, L:R.48 Hydrogen bonds: I:N.39, I:N.39, M:Y.58 CDL.8: 21 residues within 4Å: Chain 2: P.5, L.6, V.9 Chain Q: P.3, Y.6, T.7, T.8, I.10, M.11, M.14, K.46, Q.125, L.128, L.129, T.132, W.133, L.206, L.213, M.217, K.321, L.325 13 PLIP interactions: 12 interactions with chain Q, 1 interactions with chain 2 Hydrophobic interactions: Q:I.10, Q:L.128, Q:L.129, Q:T.132, Q:W.133, Q:W.133, Q:L.206, Q:L.325, 2:V.9 Hydrogen bonds: Q:Y.6, Q:Q.125 Salt bridges: Q:K.46, Q:K.321 CDL.14: 28 residues within 4Å: Chain I: L.17 Chain T: I.19, M.20, S.22, Y.27, L.78, R.116, K.119, Y.120, L.123, I.126, I.130, L.153 Chain Y: P.353, L.354, T.357, W.358, V.361, L.364, L.369, P.370, P.371, L.445, T.448, L.449 Ligands: CDL.5, PEE.6, PLX.21 21 PLIP interactions: 12 interactions with chain Y, 9 interactions with chain T Hydrophobic interactions: Y:W.358, Y:V.361, Y:L.364, Y:L.369, Y:P.371, Y:L.445, Y:L.445, Y:L.445, Y:T.448, Y:L.449, T:L.78, T:L.123, T:I.126, T:L.153 Hydrogen bonds: Y:T.357, Y:T.357, T:Y.120 Salt bridges: T:R.116, T:K.119, T:K.119, T:K.119 CDL.15: 20 residues within 4Å: Chain K: F.109, M.110 Chain T: L.290, I.293, T.294, L.413, S.417, L.418, A.421, R.425, F.429, M.496, L.500, A.501, L.504, K.514, P.516, S.517, T.519, Y.520 15 PLIP interactions: 14 interactions with chain T, 1 interactions with chain K Hydrophobic interactions: T:I.293, T:L.413, T:L.418, T:A.421, T:L.500, T:L.500, T:A.501, T:L.504, T:T.519, K:F.109 Hydrogen bonds: T:S.517, T:Y.520, T:Y.520 Salt bridges: T:R.425, T:K.514 CDL.17: 21 residues within 4Å: Chain D: L.33, A.37, I.40, P.45, S.47, F.48, G.51, T.55 Chain S: M.21, R.23 Chain T: K.585, L.592, I.593, I.595, M.596 Chain U: S.21, K.23, T.88, A.92, S.95, M.99 14 PLIP interactions: 1 interactions with chain S, 5 interactions with chain D, 4 interactions with chain T, 4 interactions with chain U Salt bridges: S:R.23, T:K.585, U:K.23 Hydrophobic interactions: D:L.33, D:L.33, D:I.40, D:F.48, D:T.55, T:L.592, T:I.593, T:I.595, U:T.88, U:A.92 Hydrogen bonds: U:T.88 CDL.19: 15 residues within 4Å: Chain 0: F.168, W.169, T.170, M.171 Chain O: T.28, P.30, R.31, Y.34 Chain Q: P.256, L.337, P.338 Chain V: L.25, R.28, K.32 Ligands: CDL.22 11 PLIP interactions: 3 interactions with chain V, 2 interactions with chain Q, 2 interactions with chain O, 4 interactions with chain 0 Hydrophobic interactions: V:L.25, Q:P.256, Q:L.337, O:Y.34, O:Y.34, 0:F.168, 0:F.168 Salt bridges: V:R.28, V:K.32 Hydrogen bonds: 0:T.170, 0:T.170 CDL.22: 30 residues within 4Å: Chain 2: Y.304 Chain O: F.37, C.41, L.44, I.45, A.48, V.54, V.55 Chain Q: P.238, V.239, S.242, L.243, M.245, V.246, T.334, L.335 Chain V: W.10, L.14 Chain Y: T.9, W.16, T.90, R.91, L.94, T.97, M.98, L.104, V.127, I.131, R.135 Ligands: CDL.19 21 PLIP interactions: 4 interactions with chain Q, 7 interactions with chain O, 6 interactions with chain Y, 2 interactions with chain V, 2 interactions with chain 2 Hydrophobic interactions: Q:L.243, Q:V.246, Q:L.335, Q:L.335, O:F.37, O:L.44, O:I.45, O:A.48, O:V.54, O:V.55, Y:T.9, Y:W.16, Y:T.97, Y:L.104, Y:I.131, V:W.10, V:L.14 Hydrogen bonds: O:V.54, Y:T.90, 2:Y.304, 2:Y.304 CDL.24: 19 residues within 4Å: Chain U: I.12, I.15, G.16, Y.28, V.35, V.82, W.83, V.84, F.93, L.97 Chain Z: R.62, S.67, I.68, S.69, I.72, I.73, L.111 Ligands: PEE.3, PEE.23 18 PLIP interactions: 6 interactions with chain Z, 12 interactions with chain U Hydrophobic interactions: Z:I.68, Z:I.72, Z:L.111, U:I.12, U:I.15, U:W.83, U:W.83, U:W.83, U:V.84, U:F.93, U:F.93, U:L.97 Hydrogen bonds: Z:R.62, Z:S.69, Z:S.69, U:Y.28, U:W.83, U:V.84

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

PEE.3: 22 residues within 4Å: Chain B: A.39 Chain E: F.109, I.110, W.111, Y.112, T.113 Chain R: I.3, M.4 Chain U: I.12, V.39, G.42, L.45, N.46, S.50, F.57 Chain Z: M.98, N.99, L.100, F.104, M.108 Ligands: PEE.23, CDL.24 9 PLIP interactions: 5 interactions with chain U, 3 interactions with chain Z, 1 interactions with chain B Hydrophobic interactions: U:I.12, U:V.39, U:F.57, Z:F.104 Hydrogen bonds: U:S.50, U:S.50, Z:N.99, Z:L.100, B:A.39 PEE.6: 13 residues within 4Å: Chain J: I.80, Y.84, H.88 Chain T: W.66, H.67, W.68, L.78, F.138 Chain Y: P.371, L.449 Ligands: CDL.5, CDL.14, PLX.21 14 PLIP interactions: 8 interactions with chain T, 2 interactions with chain Y, 4 interactions with chain J Hydrophobic interactions: T:W.66, T:W.66, T:W.66, T:W.66, T:L.78, T:F.138, Y:P.371, Y:L.449, J:I.80, J:Y.84 Hydrogen bonds: T:H.67, T:H.67 Salt bridges: J:H.88, J:K.92 PEE.9: 19 residues within 4Å: Chain A: M.19, Y.20 Chain Q: M.284, L.287, L.288, Y.291, R.295 Chain T: L.562, P.563, T.566, S.567, Q.570, M.571 Chain Y: L.147, Y.148, F.151, Y.152, A.155 Ligands: PEE.20 13 PLIP interactions: 2 interactions with chain T, 4 interactions with chain Y, 7 interactions with chain Q Hydrophobic interactions: T:L.562, T:T.566, Y:L.147, Y:Y.148, Y:F.151, Y:Y.152, Q:L.287, Q:L.288, Q:Y.291, Q:Y.291, Q:Y.291 Hydrogen bonds: Q:Y.291 Salt bridges: Q:R.295 PEE.10: 18 residues within 4Å: Chain C: F.7, L.8, A.11, E.15, L.18, V.19, F.22, A.23, G.25, I.29 Chain R: A.99, L.102, A.103, W.106, T.107 Chain Z: K.291, P.295, M.302 22 PLIP interactions: 5 interactions with chain R, 15 interactions with chain C, 2 interactions with chain Z Hydrophobic interactions: R:A.99, R:L.102, R:A.103, C:F.7, C:F.7, C:L.8, C:A.11, C:L.18, C:L.18, C:V.19, C:V.19, C:F.22, C:F.22, C:F.22, C:F.22, C:F.22, C:A.23, C:I.29, Z:P.295 Hydrogen bonds: R:W.106 Salt bridges: R:K.109, Z:K.291 PEE.13: 6 residues within 4Å: Chain D: I.109, A.112, Y.116 Chain T: F.568, K.572, M.573 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain T Hydrophobic interactions: D:I.109, D:Y.116, D:Y.116, T:F.568, T:K.572 Salt bridges: T:K.572 PEE.16: 17 residues within 4Å: Chain K: N.85, R.86 Chain T: D.163, T.166, Q.170, L.173, Y.174, I.177, I.180, G.228, L.229, M.533, H.534, T.538, N.541 Chain Y: M.401, L.405 10 PLIP interactions: 8 interactions with chain T, 1 interactions with chain K, 1 interactions with chain Y Hydrophobic interactions: T:L.173, T:I.177, T:I.180, T:H.534, K:R.86, Y:L.405 Hydrogen bonds: T:D.163, T:Q.170 Salt bridges: T:H.534, T:H.534 PEE.20: 17 residues within 4Å: Chain D: L.123, E.130, W.132 Chain Q: I.276, I.277 Chain T: L.562 Chain Y: Y.152, A.155, P.159, Y.166, S.191, F.194, M.195, L.197, A.198, V.205 Ligands: PEE.9 11 PLIP interactions: 3 interactions with chain D, 1 interactions with chain Q, 6 interactions with chain Y, 1 interactions with chain T Hydrophobic interactions: D:L.123, D:W.132, Q:I.276, Y:P.159, Y:F.194, Y:L.197, Y:L.197, Y:A.198, Y:V.205, T:L.562 Hydrogen bonds: D:E.130 PEE.23: 13 residues within 4Å: Chain R: S.15, V.18, L.19, F.22, W.23 Chain Z: R.62, I.72, I.73, I.76, L.77, L.81 Ligands: PEE.3, CDL.24 9 PLIP interactions: 7 interactions with chain Z, 2 interactions with chain R Hydrophobic interactions: Z:I.72, Z:I.72, Z:I.73, Z:I.76, Z:L.77, Z:L.81, R:V.18, R:W.23 Salt bridges: Z:R.62 PEE.25: 13 residues within 4Å: Chain C: V.17, I.24 Chain E: L.12 Chain Z: M.183, F.186, I.187, I.273, Y.277, L.288, S.292, F.293, L.296, W.303 9 PLIP interactions: 7 interactions with chain Z, 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: Z:F.186, Z:F.186, Z:Y.277, Z:F.293, Z:L.296, Z:W.303, C:I.24, E:L.12 Hydrogen bonds: Z:S.292

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

8Q1.4: 20 residues within 4Å: Chain F: D.43, S.44, L.45 Chain T: Y.515 Chain X: H.11, Q.12, V.15, A.22, M.43, F.47, H.50, K.51, E.53, A.59, L.62, L.63, A.66, E.69, F.70, G.73 15 PLIP interactions: 13 interactions with chain X, 2 interactions with chain F Hydrophobic interactions: X:Q.12, X:V.15, X:A.22, X:F.47, X:A.59, X:A.66, X:F.70, X:F.70 Hydrogen bonds: X:Q.12, X:K.51, X:K.51, X:K.51, F:S.44, F:L.45 Salt bridges: X:K.51

5 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: 21 residues within 4Å: Chain O: S.4, R.9, P.11, L.12, F.14, M.35, F.72, L.76, R.79 Chain P: P.1, F.2 Chain Q: I.202, L.203, I.207, L.332, V.336, M.339, A.342, L.343, S.345, L.346 12 PLIP interactions: 6 interactions with chain O, 6 interactions with chain Q Hydrophobic interactions: O:F.72, O:F.72, O:L.76, Q:L.203, Q:I.207, Q:L.332, Q:V.336, Q:M.339, Q:A.342 Hydrogen bonds: O:L.12 Salt bridges: O:R.9, O:R.79 PLX.11: 6 residues within 4Å: Chain R: L.16, I.20, W.23, L.24, P.25, Q.26 4 PLIP interactions: 4 interactions with chain R Hydrophobic interactions: R:L.16, R:I.20, R:W.23, R:L.24 PLX.12: 11 residues within 4Å: Chain P: L.13 Chain R: N.83, T.86, T.89, F.93 Chain U: S.148, Y.149, T.151, W.152, I.155, W.159 11 PLIP interactions: 4 interactions with chain R, 6 interactions with chain U, 1 interactions with chain P Hydrophobic interactions: R:F.93, R:F.93, U:T.151, U:W.152, U:I.155, U:I.155, U:W.159, P:L.13 Hydrogen bonds: R:N.83, R:T.86 pi-Cation interactions: U:Y.149 PLX.18: 13 residues within 4Å: Chain I: I.66, R.72, T.73, F.74, Y.75, D.76 Chain M: T.54, F.55 Chain V: F.19, R.27 Chain Y: L.36, I.37, S.40 13 PLIP interactions: 4 interactions with chain Y, 2 interactions with chain V, 3 interactions with chain M, 4 interactions with chain I Hydrogen bonds: Y:S.40, Y:S.40 Salt bridges: Y:K.3, Y:K.3, V:R.27, I:D.76 Hydrophobic interactions: V:F.19, M:T.54, M:F.55, M:F.55, I:I.66, I:F.74, I:F.74 PLX.21: 19 residues within 4Å: Chain M: S.53, V.56, A.57, Y.58 Chain T: M.20, N.23, W.66 Chain Y: L.39, P.64, V.67, W.71, P.443, L.446, L.447, N.450, I.454 Ligands: CDL.5, PEE.6, CDL.14 8 PLIP interactions: 6 interactions with chain Y, 1 interactions with chain T, 1 interactions with chain M Hydrophobic interactions: Y:L.39, Y:W.71, Y:P.443, Y:N.450, Y:I.454, T:N.23, M:V.56 Hydrogen bonds: Y:N.450

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

ADP.26: 15 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 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

2022-11-23

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
Complex I-B17: 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
Complex I-B18: 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

Complex I-B17

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

Complex I-B18

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

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