SMTL ID : 7vys.1

Membrane arm of active state CI from Q1-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: 20 residues within 4Å: Chain C: V.17, I.24 Chain E: I.9, L.12 Chain Z: P.180, A.182, M.183, M.184, F.186, I.187, P.197, F.198, I.273, Y.277, F.280, L.288, S.292, F.293, L.296, W.303 12 PLIP interactions: 1 interactions with chain C, 9 interactions with chain Z, 2 interactions with chain E Hydrophobic interactions: C:I.24, Z:F.186, Z:P.197, Z:F.198, Z:I.273, Z:I.273, Z:Y.277, Z:F.280, Z:F.293, Z:W.303, E:I.9, E:L.12 PEE.4: 19 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.35, V.39, L.45, S.50, F.57 Chain Z: M.98, N.99, F.104, M.108 Ligands: CDL.25 12 PLIP interactions: 2 interactions with chain R, 3 interactions with chain Z, 6 interactions with chain U, 1 interactions with chain E Hydrophobic interactions: R:I.3, R:I.3, Z:F.104, U:I.12, U:V.35, U:L.45, U:F.57 Hydrogen bonds: Z:N.99, Z:N.99, U:S.50, E:Y.112 Water bridges: U:S.50 PEE.10: 19 residues within 4Å: Chain A: Q.13, Y.20 Chain Q: L.170, M.284, L.287, L.288, Y.291, R.295 Chain T: L.562, T.566, S.567, Q.570, M.571 Chain Y: N.144, L.147, F.151, Y.152, A.155 Ligands: PEE.22 10 PLIP interactions: 6 interactions with chain Q, 3 interactions with chain Y, 1 interactions with chain T Hydrophobic interactions: Q:L.287, Q:Y.291, Q:Y.291, Q:Y.291, Y:L.147, Y:F.151, Y:Y.152, T:L.562 Hydrogen bonds: Q:Y.291 Salt bridges: Q:R.295 PEE.12: 17 residues within 4Å: Chain C: F.7, L.8, E.15, L.18, F.22, A.23, G.25, G.26, I.29 Chain R: A.99, A.103, W.106, T.107 Chain Z: K.291, P.295, A.299, M.302 19 PLIP interactions: 7 interactions with chain R, 9 interactions with chain C, 3 interactions with chain Z Hydrophobic interactions: R:A.99, R:A.103, R:W.106, R:W.106, R:W.106, R:T.107, C:F.7, C:L.8, C:E.15, C:L.18, C:L.18, C:L.18, C:F.22, C:A.23, C:I.29, Z:P.295, Z:A.299 Hydrogen bonds: R:W.106 Salt bridges: Z:K.291 PEE.13: 12 residues within 4Å: Chain R: V.11, S.15, V.18, L.19, F.22, W.23 Chain Z: I.72, I.76, L.77, S.80 Ligands: PLX.14, CDL.25 9 PLIP interactions: 6 interactions with chain R, 3 interactions with chain Z Hydrophobic interactions: R:V.11, R:V.11, R:V.18, R:L.19, Z:I.72, Z:I.72, Z:I.76 Water bridges: R:F.22, R:W.23 PEE.17: 9 residues within 4Å: Chain D: I.109, A.112, Y.116, T.120 Chain Q: W.167 Chain T: F.568, I.569, K.572, M.573 6 PLIP interactions: 4 interactions with chain T, 2 interactions with chain D Hydrophobic interactions: T:I.569, T:I.569, D:Y.116, D:Y.116 Salt bridges: T:K.572, T:K.572 PEE.20: 19 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, L.280, M.533, H.534, T.538, N.541, L.542 Chain Y: M.398, M.401 15 PLIP interactions: 14 interactions with chain T, 1 interactions with chain K Hydrophobic interactions: T:L.173, T:Y.174, T:I.177, T:I.180, T:L.229, T:L.280, T:H.534, T:T.538, T:N.541, T:L.542, K:R.86 Hydrogen bonds: T:D.163, T:Q.170 Salt bridges: T:H.534, T:H.534 PEE.21: 11 residues within 4Å: Chain J: I.80, Y.84, H.88 Chain T: W.66, H.67, W.68, L.78 Chain Y: L.449 Ligands: CDL.6, PLX.8, CDL.18 9 PLIP interactions: 1 interactions with chain J, 7 interactions with chain T, 1 interactions with chain Y Salt bridges: J:H.88 Hydrophobic interactions: T:W.66, T:W.68, T:L.78, T:L.78, Y:L.449 Hydrogen bonds: T:W.66, T:H.67, T:W.68 PEE.22: 20 residues within 4Å: Chain D: E.130, G.131, W.132 Chain Q: E.274, I.276, I.277 Chain T: L.562 Chain Y: Y.152, A.155, G.156, P.159, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Ligands: PEE.10, PLX.23 13 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain D, 8 interactions with chain Y, 1 interactions with chain T Hydrophobic interactions: Q:I.277, D:W.132, Y:A.155, Y:P.159, Y:F.194, Y:F.194, Y:L.197, Y:A.198, Y:M.201, T:L.562 Hydrogen bonds: Q:E.274, D:G.131, Y:S.191

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 24 residues within 4Å: Chain D: Y.8, A.30, 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, F.113, L.153, T.156, M.157 Chain T: M.576, Q.580, I.597, F.602 19 PLIP interactions: 12 interactions with chain D, 4 interactions with chain Q, 3 interactions with chain T Hydrophobic interactions: D:Y.8, D:A.30, D:I.34, D:I.34, D:Y.38, D:Y.38, D:Y.38, D:Y.38, D:L.42, D:I.65, D:F.69, Q:P.110, Q:F.113, Q:L.153, Q:T.156, T:I.597, T:F.602 Salt bridges: D:R.57 Hydrogen bonds: T:Q.580 CDL.3: 15 residues within 4Å: Chain D: Y.107, G.108 Chain T: W.557, L.558, I.561 Chain W: P.81, T.82, P.83, S.86, L.87, G.89, A.90, G.93 Chain Y: Y.210, L.264 10 PLIP interactions: 2 interactions with chain Y, 3 interactions with chain D, 4 interactions with chain T, 1 interactions with chain W Hydrophobic interactions: Y:Y.210, Y:L.264, D:Y.107, T:W.557, T:W.557, T:L.558, T:I.561, W:L.87 Hydrogen bonds: D:Y.107, D:Y.107 CDL.6: 30 residues within 4Å: Chain I: I.24, L.25, G.28, I.29, A.32, I.35, T.36, N.39, V.40, E.44, H.64 Chain J: W.79, I.81, Y.83, Y.84, H.88 Chain L: P.43, V.44, A.47, R.48, I.51, H.55 Chain M: V.50, S.53, Y.58 Chain T: T.13, N.65, F.80 Ligands: PLX.8, PEE.21 26 PLIP interactions: 10 interactions with chain J, 8 interactions with chain I, 4 interactions with chain L, 2 interactions with chain T, 2 interactions with chain M Hydrophobic interactions: J:W.79, J:W.79, J:I.81, J:Y.83, J:Y.83, J:Y.83, J:Y.84, J:Y.84, J:Y.84, I:I.24, I:I.24, I:L.25, I:I.29, I:A.32, L:P.43, L:V.44, L:A.47, T:T.13, T:F.80, M:V.50 Salt bridges: J:H.88, I:H.64 Hydrogen bonds: I:N.39, I:N.39, L:R.48, M:Y.58 CDL.11: 33 residues within 4Å: Chain 2: K.303, Y.304 Chain O: F.38, Y.41, C.42, L.45, I.46, A.49, P.54, V.55, V.56 Chain Q: P.238, V.239, S.242, L.243, M.245, V.246, L.257, T.334, L.335 Chain V: L.14 Chain Y: P.13, W.16, M.17, T.90, R.91, L.94, T.97, M.98, L.104, V.127, R.135 Ligands: CDL.27 21 PLIP interactions: 4 interactions with chain Q, 6 interactions with chain O, 7 interactions with chain Y, 3 interactions with chain 2, 1 interactions with chain V Hydrophobic interactions: Q:L.243, Q:V.246, Q:L.257, Q:L.335, O:L.45, O:I.46, O:A.49, O:V.55, O:V.56, Y:P.13, Y:W.16, Y:W.16, Y:L.94, Y:T.97, Y:L.104, Y:V.127, V:L.14 Hydrogen bonds: O:V.55, 2:Y.304, 2:Y.304 Salt bridges: 2:K.303 CDL.16: 26 residues within 4Å: Chain D: L.33, S.36, A.37, I.40, P.44, P.45, A.46, S.47, F.48, G.51, T.55 Chain S: A.13, I.14, A.17, M.21, Y.22, R.23 Chain T: K.585, L.589, L.592, I.593 Chain U: S.21, K.23, T.88, A.92, S.95 16 PLIP interactions: 6 interactions with chain D, 4 interactions with chain T, 3 interactions with chain S, 3 interactions with chain U Hydrophobic interactions: D:L.33, D:A.37, D:I.40, D:F.48, D:F.48, D:T.55, T:L.592, T:I.593, T:I.593, S:I.14, S:M.21, U:T.88 Salt bridges: T:K.585, S:R.23, U:K.23 Hydrogen bonds: U:T.88 CDL.18: 34 residues within 4Å: Chain I: L.17 Chain T: T.16, I.19, M.20, S.22, N.23, Y.27, L.78, R.116, K.119, Y.120, L.123, I.126, T.127, I.130, I.142, 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, L.446, T.448, L.449 Ligands: PLX.8, PEE.21 20 PLIP interactions: 8 interactions with chain Y, 12 interactions with chain T Hydrophobic interactions: Y:V.361, Y:T.365, Y:L.446, Y:T.448, Y:L.449, Y:L.449, T:I.19, T:L.78, T:L.123, T:I.126, T:T.127, T:I.142, T:L.153 Hydrogen bonds: Y:P.353, Y:T.357, T:Y.120 Salt bridges: T:R.116, T:K.119, T:K.119, T:K.119 CDL.19: 21 residues within 4Å: Chain K: F.106, F.109 Chain T: L.286, L.290, I.293, T.294, L.413, I.414, S.417, L.418, A.421, R.425, F.429, V.493, L.500, L.504, K.514, S.517, T.519, Y.520, S.523 21 PLIP interactions: 4 interactions with chain K, 17 interactions with chain T Hydrophobic interactions: K:F.106, K:F.106, K:F.109, K:F.109, T:L.286, T:L.290, T:I.293, T:L.413, T:I.414, T:L.418, T:L.418, T:A.421, T:V.493, T:L.500, T:L.500, T:T.519 Hydrogen bonds: T:S.517, T:Y.520, T:Y.520 Salt bridges: T:R.425, T:K.514 CDL.25: 22 residues within 4Å: Chain U: I.12, I.15, G.16, G.19, Y.28, L.31, G.32, I.34, V.35, V.82, W.83, V.84, F.93, L.97 Chain Z: R.62, I.68, S.69, I.72, I.73, W.118 Ligands: PEE.4, PEE.13 24 PLIP interactions: 8 interactions with chain Z, 16 interactions with chain U Hydrophobic interactions: Z:I.68, Z:I.72, Z:W.118, U:I.12, U:I.15, U:L.31, U:V.35, U:V.35, U:W.83, U:W.83, U:W.83, U:W.83, U:V.84, U:F.93, U:F.93, U:L.97 Hydrogen bonds: Z:I.68, Z:S.69, Z:S.69, U:W.83, U:V.84 Water bridges: Z:M.70, U:Y.28 Salt bridges: Z:R.62 CDL.27: 16 residues within 4Å: Chain 0: F.168, W.169, T.170, M.171 Chain O: T.29, P.31, R.32, V.34, Y.35 Chain Q: P.256, P.338 Chain V: L.25, R.28, K.32 Chain Y: I.120 Ligands: CDL.11 15 PLIP interactions: 5 interactions with chain 0, 4 interactions with chain V, 1 interactions with chain Y, 3 interactions with chain Q, 2 interactions with chain O Hydrophobic interactions: 0:F.168, 0:F.168, 0:W.169, V:L.25, Y:I.120, Q:P.256, Q:P.338, Q:P.338, O:Y.35, O:Y.35 Hydrogen bonds: 0:T.170, 0:T.170 Salt bridges: V:R.28, V:K.32, V:K.32

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

8Q1.5: 17 residues within 4Å: Chain F: S.44, L.45 Chain T: Y.515 Chain X: H.11, Q.12, V.15, A.22, R.46, F.47, H.50, K.51, E.53, A.59, A.66, E.69, F.70, G.73 12 PLIP interactions: 9 interactions with chain X, 2 interactions with chain F, 1 interactions with chain T Hydrophobic interactions: X:Q.12, X:V.15, X:A.22, X:R.46, X:E.69, X:F.70, T:Y.515 Hydrogen bonds: X:Q.12, X:H.50, X:K.51, F:S.44, F:L.45

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: 16 residues within 4Å: Chain I: I.66, R.72, T.73, F.74, Y.75, D.76 Chain M: F.42, L.51, F.55 Chain V: F.19, C.23, R.27 Chain Y: L.33, L.36, I.37, S.40 14 PLIP interactions: 4 interactions with chain I, 6 interactions with chain Y, 3 interactions with chain M, 1 interactions with chain V Hydrophobic interactions: I:I.66, I:F.74, I:F.74, Y:L.33, Y:I.37, M:F.42, M:F.55, M:F.55 Salt bridges: I:D.76, Y:K.3, Y:K.3, V:R.27 Hydrogen bonds: Y:S.40, Y:S.40 PLX.8: 20 residues within 4Å: Chain M: S.53, V.56, A.57, Y.58 Chain T: N.23, W.66 Chain Y: L.39, P.64, V.67, L.68, W.71, I.317, P.443, L.446, L.447, L.449, N.450 Ligands: CDL.6, CDL.18, PEE.21 10 PLIP interactions: 9 interactions with chain Y, 1 interactions with chain M Hydrophobic interactions: Y:L.39, Y:W.71, Y:W.71, Y:I.317, Y:P.443, Y:L.446, Y:L.449, Y:N.450, M:V.56 Hydrogen bonds: Y:N.450 PLX.9: 23 residues within 4Å: Chain O: S.5, R.10, P.12, L.13, F.15, M.36, F.73, L.77, R.80 Chain P: P.1, F.2, F.3 Chain Q: L.203, I.207, T.210, M.261, L.332, V.336, M.339, A.342, L.343, S.345, L.346 16 PLIP interactions: 9 interactions with chain Q, 7 interactions with chain O Hydrophobic interactions: Q:L.203, Q:I.207, Q:T.210, Q:L.332, Q:L.332, Q:L.332, Q:M.339, Q:A.342, Q:L.346, O:F.15, O:F.15, O:F.73, O:F.73, O:L.77 Salt bridges: O:R.10, O:R.80 PLX.14: 8 residues within 4Å: Chain R: L.16, L.17, L.19, I.20, W.23, L.24, P.25 Ligands: PEE.13 6 PLIP interactions: 6 interactions with chain R Hydrophobic interactions: R:L.16, R:L.16, R:L.17, R:L.19, R:W.23, R:W.23 PLX.15: 10 residues within 4Å: Chain R: N.83, T.86, F.93, L.97 Chain U: S.148, Y.149, T.151, W.152, I.155, W.159 9 PLIP interactions: 4 interactions with chain U, 5 interactions with chain R Hydrophobic interactions: U:W.152, U:I.155, U:W.159, R:F.93, R:L.97 pi-Cation interactions: U:Y.149 Hydrogen bonds: R:N.83, R:T.86, R:T.86 PLX.23: 15 residues within 4Å: Chain D: D.85, F.90, A.122 Chain Y: N.188, S.189, W.190, I.193, M.201, L.209, L.212, Y.256, P.260, F.261, L.264 Ligands: PEE.22 13 PLIP interactions: 10 interactions with chain Y, 3 interactions with chain D Hydrophobic interactions: Y:W.190, Y:I.193, Y:I.193, Y:L.209, Y:L.212, Y:Y.256, Y:P.260, Y:F.261, Y:F.261, D:F.90, D:F.90, D:A.122 pi-Cation interactions: Y:W.190

1 x TYR: TYROSINE(Covalent)

TYR.24: 10 residues within 4Å: Chain M: R.63 Chain T: M.69, T.70, Q.72 Chain Y: M.310, K.452, L.455, G.456, P.457, L.458 4 PLIP interactions: 2 interactions with chain T, 2 interactions with chain Y Hydrogen bonds: T:T.70, T:Q.72, Y:G.456 Hydrophobic interactions: Y:L.455

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

UQ.26: 9 residues within 4Å: Chain Z: L.14, R.25, D.51, A.52, L.55, A.221, F.224, M.225, R.274 9 PLIP interactions: 9 interactions with chain Z Hydrophobic interactions: Z:L.14, Z:D.51, Z:A.221, Z:F.224, Z:F.224, Z:F.224 Hydrogen bonds: Z:R.274 Water bridges: Z:Y.228 pi-Cation interactions: Z:R.274

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

ADP.28: 14 residues within 4Å: Chain 2: N.30, I.31, C.32, K.35, E.53, L.79, Y.83, Q.97, L.100, R.104, R.126, D.131, F.134, E.191 14 PLIP interactions: 14 interactions with chain 2 Hydrogen bonds: 2:N.30, 2:C.32, 2:Y.83, 2:Q.97, 2:Q.97, 2:R.104, 2:R.104, 2:R.126, 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, mitochondrial: 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.
Show / Hide

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, mitochondrial

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

Related Entries With Identical Sequence