SMTL ID : 7vbl.1

Membrane arm of active state CI from DQ-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: 16 residues within 4Å: Chain C: F.7, E.15, L.18, S.21, F.22, A.23, G.25, G.26 Chain R: A.99, A.103, W.106, T.107 Chain Z: K.291, P.295, L.298, M.302 10 PLIP interactions: 2 interactions with chain Z, 4 interactions with chain C, 4 interactions with chain R Hydrophobic interactions: Z:L.298, C:F.7, C:F.22, C:F.22, C:A.23, R:A.99, R:W.106, R:W.106 Salt bridges: Z:K.291 Hydrogen bonds: R:W.106 PEE.2: 20 residues within 4Å: Chain C: E.15, V.17, I.24 Chain E: I.9, L.12 Chain Z: W.179, P.180, A.182, M.183, M.184, F.186, I.187, F.198, I.273, Y.277, L.288, S.292, F.293, L.296, W.303 16 PLIP interactions: 12 interactions with chain Z, 2 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: Z:W.179, Z:P.180, Z:F.186, Z:F.186, Z:F.186, Z:I.187, Z:F.198, Z:I.273, Z:Y.277, Z:F.293, Z:L.296, Z:W.303, E:I.9, E:L.12, C:I.24 Hydrogen bonds: C:E.15 PEE.5: 21 residues within 4Å: Chain B: A.39 Chain E: F.109, I.110, Y.112, T.113 Chain R: I.3 Chain U: I.12, V.35, G.38, V.39, C.41, G.42, L.45, N.46, S.50, F.57 Chain Z: M.98, N.99, F.104, M.108 Ligands: CDL.25 13 PLIP interactions: 7 interactions with chain U, 2 interactions with chain R, 3 interactions with chain Z, 1 interactions with chain E Hydrophobic interactions: U:I.12, U:V.35, U:V.39, U:L.45, U:F.57, R:I.3, R:I.3, Z:F.104 Hydrogen bonds: U:S.50, U:S.50, Z:N.99, Z:N.99, E:Y.112 PEE.11: 19 residues within 4Å: Chain A: Q.13, M.19, Y.20 Chain Q: L.163, L.170, M.284, T.285, L.287, L.288, Y.291, R.295 Chain T: L.562, T.566, S.567, Q.570 Chain Y: N.144, F.151, Y.152, A.155 16 PLIP interactions: 7 interactions with chain Q, 3 interactions with chain T, 4 interactions with chain Y, 2 interactions with chain A Hydrophobic interactions: Q:L.163, Q:L.287, Q:L.288, Q:Y.291, Q:Y.291, T:L.562, T:L.562, T:T.566, Y:F.151, Y:F.151, Y:Y.152, Y:A.155 Hydrogen bonds: Q:Y.291, A:Q.13, A:Y.20 Salt bridges: Q:R.295 PEE.12: 13 residues within 4Å: Chain R: V.11, S.15, V.18, L.19, F.22, W.23, L.27 Chain Z: I.73, I.76, L.77, S.80 Ligands: PLX.13, CDL.25 6 PLIP interactions: 5 interactions with chain R, 1 interactions with chain Z Hydrophobic interactions: R:V.11, R:V.18, R:L.19, R:W.23, R:W.23, Z:I.73 PEE.15: 8 residues within 4Å: Chain D: I.109, A.112, A.113, Y.116 Chain Q: W.167 Chain T: F.568, I.569, M.573 6 PLIP interactions: 4 interactions with chain D, 1 interactions with chain Q, 1 interactions with chain T Hydrophobic interactions: D:I.109, D:A.112, D:A.113, D:Y.116, Q:W.167, T:I.569 PEE.17: 18 residues within 4Å: Chain K: N.85, R.86 Chain T: D.163, T.166, Q.170, L.173, Y.174, I.180, A.221, G.228, L.229, L.280, Y.529, M.533, H.534, T.538, N.541 Chain Y: L.405 14 PLIP interactions: 12 interactions with chain T, 1 interactions with chain Y, 1 interactions with chain K Hydrophobic interactions: T:L.173, T:Y.174, T:I.180, T:A.221, T:L.229, T:L.280, T:T.538, T:N.541, Y:L.405, K:R.86 Hydrogen bonds: T:D.163, T:Q.170 Salt bridges: T:H.534, T:H.534 PEE.18: 15 residues within 4Å: Chain J: I.80, Y.83, Y.84, H.88 Chain T: N.65, W.66, H.67, W.68, S.77, L.78, N.136 Chain Y: L.449 Ligands: CDL.7, PLX.22, CDL.23 15 PLIP interactions: 6 interactions with chain J, 1 interactions with chain Y, 8 interactions with chain T Hydrophobic interactions: J:I.80, J:I.80, J:Y.83, J:Y.84, Y:L.449, T:W.66, T:W.66, T:W.68, T:L.78, T:L.78 Salt bridges: J:H.88, J:K.92 Hydrogen bonds: T:N.65, T:H.67, T:H.67 PEE.20: 18 residues within 4Å: Chain D: L.123, E.130, G.131, W.132 Chain Q: I.276, I.277 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: PLX.21 12 PLIP interactions: 4 interactions with chain D, 7 interactions with chain Y, 1 interactions with chain Q Hydrophobic interactions: D:L.123, D:L.123, D:W.132, Y:A.155, Y:F.194, Y:F.194, Y:L.197, Y:A.198, Y:M.201, Q:I.276 Hydrogen bonds: D:E.130, Y:S.191

10 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 27 residues within 4Å: Chain D: S.24, I.27, G.28, 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, T.156, M.157, L.160, I.164 Chain T: M.576, Q.580, I.597 21 PLIP interactions: 13 interactions with chain D, 6 interactions with chain Q, 2 interactions with chain T Hydrophobic interactions: D:I.27, D:I.34, D:V.35, 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, Q:L.160, Q:I.164, T:I.597 Hydrogen bonds: D:R.57, D:Y.58, T:Q.580 Salt bridges: D:K.43 CDL.4: 16 residues within 4Å: Chain D: Y.107, G.108 Chain T: W.557, L.558 Chain W: P.81, T.82, P.83, S.86, L.87, G.89, A.90, G.93, L.97 Chain Y: Y.210, L.264 Ligands: PLX.21 12 PLIP interactions: 2 interactions with chain T, 6 interactions with chain W, 2 interactions with chain Y, 2 interactions with chain D Hydrophobic interactions: T:W.557, T:L.558, W:P.83, W:P.83, W:L.87, W:A.90, W:L.97, Y:Y.210, Y:L.264 Hydrogen bonds: W:S.86, D:Y.107, D:Y.107 CDL.7: 33 residues within 4Å: Chain I: I.24, L.25, G.28, A.32, T.36, N.39, V.40, E.44, H.64 Chain J: W.79, Y.83, Y.84, H.88 Chain L: P.43, A.47, R.48, I.51 Chain M: V.50, S.53, T.54, A.57, Y.58 Chain T: L.9, L.12, T.13, N.65, F.80, I.126, I.130 Chain Y: L.446 Ligands: PEE.18, PLX.22, CDL.23 23 PLIP interactions: 5 interactions with chain I, 3 interactions with chain L, 5 interactions with chain T, 2 interactions with chain M, 7 interactions with chain J, 1 interactions with chain Y Hydrophobic interactions: I:I.24, I:L.25, L:A.47, L:I.51, T:L.9, T:L.12, T:F.80, T:I.126, T:I.130, M:V.50, J:W.79, J:W.79, J:W.79, J:Y.83, J:Y.84, J:Y.84, Y:L.446 Hydrogen bonds: I:N.39, I:E.44, L:R.48, M:Y.58 Salt bridges: I:H.64, J:H.88 CDL.10: 23 residues within 4Å: Chain 2: P.5, V.9 Chain Q: P.3, Y.6, T.7, T.8, I.10, M.11, M.14, S.15, M.18, M.35, K.46, Q.125, L.128, L.129, T.132, W.133, L.136, I.209, M.217, L.325 Chain U: W.159 15 PLIP interactions: 13 interactions with chain Q, 2 interactions with chain U Hydrophobic interactions: Q:T.8, Q:I.10, Q:M.11, Q:M.18, Q:L.128, Q:L.129, Q:W.133, Q:L.136, Q:I.209, Q:L.325, U:W.159, U:W.159 Hydrogen bonds: Q:T.7, Q:Q.125 Salt bridges: Q:K.46 CDL.16: 19 residues within 4Å: Chain K: F.106, F.109, M.110 Chain T: L.286, L.290, I.293, T.294, I.414, S.417, L.418, R.425, V.493, M.496, L.500, A.501, N.505, S.517, T.519, Y.520 17 PLIP interactions: 13 interactions with chain T, 4 interactions with chain K Hydrophobic interactions: T:L.286, T:L.290, T:I.293, T:I.414, T:L.418, T:V.493, T:L.500, T:A.501, K:F.106, K:F.109, K:F.109, K:F.109 Hydrogen bonds: T:S.517, T:Y.520, T:Y.520 Salt bridges: T:R.425, T:R.425 CDL.19: 25 residues within 4Å: Chain D: A.37, I.40, P.45, S.47, F.48, G.51, V.52 Chain Q: M.97 Chain S: A.13, I.14, L.16, A.17, M.21, Y.22, R.23 Chain T: K.585, I.593, M.596 Chain U: S.21, S.22, K.23, T.88, A.92, S.95, M.99 9 PLIP interactions: 2 interactions with chain U, 3 interactions with chain S, 3 interactions with chain T, 1 interactions with chain D Hydrogen bonds: U:T.88 Salt bridges: U:K.23, S:R.23, T:K.585 Hydrophobic interactions: S:A.13, S:I.14, T:I.593, T:I.593, D:F.48 CDL.23: 28 residues within 4Å: Chain I: L.17 Chain T: T.16, I.19, M.20, Y.27, L.78, R.116, K.119, Y.120, L.123, I.126, I.130, M.150, L.153 Chain Y: P.353, L.354, T.357, V.361, T.365, L.369, P.370, P.371, S.372, L.445, L.449 Ligands: CDL.7, PEE.18, PLX.22 16 PLIP interactions: 7 interactions with chain Y, 9 interactions with chain T Hydrophobic interactions: Y:T.365, Y:P.371, Y:L.445, Y:L.445, Y:L.449, T:T.16, T:I.19, T:L.78, T:I.126, T:I.130, T:L.153 Hydrogen bonds: Y:P.353, Y:T.357, T:Y.120 Salt bridges: T:R.116, T:K.119 CDL.24: 33 residues within 4Å: Chain 2: K.303, Y.304 Chain O: F.38, Y.41, C.42, L.45, I.46, A.49, V.55, V.56 Chain Q: P.238, V.239, S.242, L.243, M.245, V.246, P.256, L.335 Chain V: L.14, V.17 Chain Y: M.10, P.13, W.16, T.90, R.91, L.94, T.97, M.98, L.101, L.104, F.105, V.127, R.135 27 PLIP interactions: 10 interactions with chain Y, 7 interactions with chain O, 4 interactions with chain Q, 4 interactions with chain 2, 2 interactions with chain V Hydrophobic interactions: Y:P.13, Y:P.13, Y:W.16, Y:L.94, Y:T.97, Y:L.101, Y:L.104, Y:F.105, Y:V.127, O:F.38, O:L.45, O:I.46, O:I.46, O:A.49, O:V.55, Q:V.246, Q:P.256, Q:L.335, Q:L.335, V:L.14, V:V.17 Hydrogen bonds: Y:T.90, O:V.55, 2:K.303, 2:Y.304, 2:Y.304 Salt bridges: 2:K.303 CDL.25: 18 residues within 4Å: Chain U: I.15, Y.28, L.31, 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.77 Ligands: PEE.5, PEE.12 20 PLIP interactions: 12 interactions with chain U, 8 interactions with chain Z Hydrophobic interactions: U:I.15, U:L.31, U:V.35, U:V.35, U:W.83, U:W.83, U:V.84, U:F.93, U:L.97, Z:I.68, Z:I.72, Z:L.77 Hydrogen bonds: U:W.83, U:V.84, Z:I.68, Z:S.69, Z:S.69 Water bridges: U:Y.28, Z:M.70 Salt bridges: Z:R.62 CDL.27: 13 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: R.28 Chain Y: L.121 9 PLIP interactions: 1 interactions with chain V, 3 interactions with chain Q, 1 interactions with chain Y, 3 interactions with chain 0, 1 interactions with chain O Salt bridges: V:R.28 Hydrophobic interactions: Q:P.256, Q:P.338, Q:P.338, Y:L.121, 0:F.168, 0:F.168, O:Y.35 Hydrogen bonds: 0:T.170

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

8Q1.6: 21 residues within 4Å: Chain F: D.43, S.44, L.45 Chain T: F.513 Chain X: H.11, Q.12, V.15, L.16, H.25, W.29, R.46, F.47, H.50, K.51, E.53, A.59, L.62, A.66, E.69, F.70, G.73 15 PLIP interactions: 12 interactions with chain X, 2 interactions with chain F, 1 interactions with chain T Hydrophobic interactions: X:Q.12, X:V.15, X:H.25, X:R.46, X:F.47, X:E.53, X:A.66, X:E.69, T:F.513 Hydrogen bonds: X:Q.12, X:H.50, X:K.51, F:S.44, F:L.45 Salt bridges: X:K.51

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.8: 15 residues within 4Å: Chain I: I.35, R.72, T.73, F.74, Y.75, D.76 Chain M: L.51, T.54, F.55 Chain V: C.23, R.27 Chain Y: K.3, L.36, I.37, S.40 13 PLIP interactions: 4 interactions with chain I, 6 interactions with chain Y, 2 interactions with chain M, 1 interactions with chain V Hydrophobic interactions: I:I.35, I:F.74, I:F.74, Y:L.36, Y:I.37, M:T.54, 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.9: 22 residues within 4Å: Chain O: S.5, R.10, P.12, L.13, Q.14, 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, L.332, V.336, M.339, A.342, L.343, S.345 13 PLIP interactions: 7 interactions with chain O, 6 interactions with chain Q Hydrophobic interactions: O:F.15, O:F.73, O:F.73, O:L.77, O:L.77, Q:L.203, Q:I.207, Q:L.332, Q:V.336, Q:M.339, Q:A.342 Salt bridges: O:R.10, O:R.80 PLX.13: 8 residues within 4Å: Chain R: L.16, L.19, I.20, W.23, L.24, P.25, Q.26 Ligands: PEE.12 6 PLIP interactions: 6 interactions with chain R Hydrophobic interactions: R:L.16, R:L.16, R:L.19, R:W.23, R:W.23, R:L.24 PLX.14: 9 residues within 4Å: Chain P: L.13 Chain R: N.83, T.86 Chain U: S.148, Y.149, T.151, W.152, I.155, W.159 7 PLIP interactions: 4 interactions with chain U, 1 interactions with chain P, 2 interactions with chain R Hydrophobic interactions: U:W.152, U:I.155, U:W.159, P:L.13 pi-Cation interactions: U:Y.149 Hydrogen bonds: R:N.83, R:T.86 PLX.21: 16 residues within 4Å: Chain D: D.85, P.86, L.87, F.90, A.122 Chain Y: N.188, S.189, W.190, I.193, M.201, Y.256, P.260, F.261, L.264 Ligands: CDL.4, PEE.20 10 PLIP interactions: 6 interactions with chain Y, 4 interactions with chain D Hydrophobic interactions: Y:W.190, Y:I.193, Y:Y.256, Y:P.260, Y:F.261, D:L.87, D:F.90, D:F.90, D:A.122 pi-Cation interactions: Y:W.190 PLX.22: 20 residues within 4Å: Chain M: V.48, 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, I.317, P.443, L.446, L.449, N.450 Ligands: CDL.7, PEE.18, CDL.23 12 PLIP interactions: 1 interactions with chain M, 10 interactions with chain Y, 1 interactions with chain T Hydrophobic interactions: M:V.56, Y:L.39, Y:L.39, Y:V.67, Y:W.71, Y:W.71, Y:I.317, Y:P.443, Y:L.446, Y:L.449, T:N.23 Hydrogen bonds: Y:N.450

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

UQ.26: 10 residues within 4Å: Chain Z: L.14, L.15, T.21, R.25, D.51, A.52, L.55, F.224, M.225, R.274 10 PLIP interactions: 10 interactions with chain Z Hydrophobic interactions: Z:L.14, Z:L.15, Z:T.21, Z:D.51, Z:A.52, Z:L.55, Z:F.224, Z:F.224, Z:F.224 pi-Cation interactions: Z:R.274

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

ADP.28: 14 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, E.191 13 PLIP interactions: 13 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, 2:K.186 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

2022-04-06

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.
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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, 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

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