SMTL ID : 5lnk.1

Entire ovine respiratory complex I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: P.204, S.359, C.360, G.361, Q.362, C.363, C.366, T.404, I.405, C.406, L.408 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.189 Metal complexes: A:C.360, A:C.363, A:C.366, A:C.406 SF4.4: 12 residues within 4Å: Chain C: H.101, D.104, C.105, C.108, G.111, C.114, L.116, Q.117, R.152, V.205, G.206 Chain D: M.324 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.104 Metal complexes: C:H.101, C:C.105, C:C.108, C:C.114 SF4.5: 10 residues within 4Å: Chain C: C.153, I.154, Q.155, C.156, T.157, R.158, C.159, C.203, P.204, V.205 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.153, C:C.156, C:C.159, C:C.203 SF4.7: 13 residues within 4Å: Chain D: R.87, H.172 Chain F: A.53, C.54, C.55, G.90, T.91, G.117, S.118, C.119, G.148, C.149, P.150 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.54, F:C.55, F:C.119, F:C.149 SF4.9: 12 residues within 4Å: Chain G: H.65, C.87, P.88, A.89, A.91, I.92, C.116, I.117, Y.118, C.119, G.120, C.122 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:E.133 Metal complexes: G:C.87, G:C.116, G:C.119, G:C.122 SF4.10: 13 residues within 4Å: Chain G: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, C.126, P.127, V.128, A.130, I.131 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.77, G:C.80, G:C.83, G:C.126

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 19 residues within 4Å: Chain A: G.68, R.69, A.72, K.79, N.97, D.99, E.100, G.101, D.108, Y.185, G.188, E.189, E.190, V.223, A.224, N.225, T.228, A.407, L.408 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.185, A:E.189, A:A.407, A:L.408 Hydrogen bonds: A:R.69, A:R.69, A:E.100, A:G.101, A:E.190, A:N.225, A:T.228 Salt bridges: A:K.79

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.3: 11 residues within 4Å: Chain A: P.103, G.104 Chain B: C.103, P.107, C.108, C.144, L.145, G.146, A.147, C.148, M.153 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.103, B:C.108, B:C.144, B:C.148 FES.6: 9 residues within 4Å: Chain C: C.41, Y.42, A.49, G.50, N.51, C.52, R.53, C.55, C.69 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.41, C:C.52, C:C.55, C:C.69

4 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.8: 22 residues within 4Å: Chain 0: V.17, I.24 Chain 4: I.39, L.42 Chain D: R.215, N.219 Chain G: T.24, L.25, L.26, W.27, L.30, I.31 Chain H: P.180, M.184, F.186, I.187, P.197, L.288, K.291, N.292, L.296, W.303 23 PLIP interactions: 9 interactions with chain G, 8 interactions with chain H, 1 interactions with chain 0, 2 interactions with chain 4, 3 interactions with chain D Hydrophobic interactions: G:L.25, G:L.25, G:L.25, G:L.26, G:W.27, G:W.27, G:W.27, G:L.30, G:I.31, H:P.180, H:F.186, H:F.186, H:F.186, H:I.187, H:P.197, H:W.303, 0:I.24, 4:I.39, 4:L.42 Hydrogen bonds: H:N.292, D:N.219 Salt bridges: D:R.215, D:R.215 3PE.17: 20 residues within 4Å: Chain 4: F.139, Y.142 Chain H: L.77, L.81, M.98, N.99, L.100, F.104 Chain J: L.3, L.7 Chain N: I.34, V.35, G.38, G.42, L.45, N.46, S.50, L.54, F.57 Chain d: H.40 15 PLIP interactions: 5 interactions with chain H, 7 interactions with chain N, 2 interactions with chain J, 1 interactions with chain d Hydrophobic interactions: H:L.77, H:L.81, H:F.104, N:I.34, N:V.35, N:L.45, N:L.45, N:F.57, N:F.57, J:L.3, J:L.7 Hydrogen bonds: H:N.99, H:L.100, N:S.50, d:H.40 3PE.23: 14 residues within 4Å: Chain 2: F.36, Y.39, L.43, V.53, L.54 Chain I: I.239, I.242 Chain K: I.6, M.9, M.10, P.13, W.16, L.17, A.90 8 PLIP interactions: 4 interactions with chain K, 4 interactions with chain 2 Hydrophobic interactions: K:I.6, K:P.13, K:W.16, K:L.17, 2:F.36, 2:Y.39, 2:V.53, 2:L.54 3PE.24: 11 residues within 4Å: Chain 2: R.60, L.63, Y.64, F.68, V.71 Chain I: T.324, L.325, T.328, L.332 Ligands: PC1.11 Chain b: K.16 4 PLIP interactions: 4 interactions with chain 2 Hydrophobic interactions: 2:Y.64, 2:F.68, 2:F.68 Salt bridges: 2:R.60

4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.11: 14 residues within 4Å: Chain I: S.125, L.128, I.129, T.132, L.136, I.206, I.209, S.213, M.220, T.324, M.329 Chain Y: P.5 Ligands: PC1.22, 3PE.24 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:L.128, I:I.129, I:L.136, I:I.206, I:I.209 Hydrogen bonds: I:S.125 PC1.12: 11 residues within 4Å: Chain 0: F.22 Chain H: P.295 Chain I: I.4 Chain J: F.96, A.99, V.100, A.103, Y.104, Q.108 Chain N: W.159 Ligands: CDL.16 4 PLIP interactions: 2 interactions with chain J, 1 interactions with chain 0, 1 interactions with chain H Hydrophobic interactions: J:F.96, J:F.96, 0:F.22, H:P.295 PC1.13: 15 residues within 4Å: Chain 2: P.29, R.30 Chain I: P.256, M.335, P.338 Chain K: L.2, T.55, F.56, L.101, F.105, F.117, M.121 Chain f: F.168, W.169, T.170 8 PLIP interactions: 3 interactions with chain K, 2 interactions with chain I, 2 interactions with chain 2, 1 interactions with chain f Hydrophobic interactions: K:L.101, K:F.105, K:F.117, I:P.256, I:P.338, 2:P.29, 2:R.30, f:F.168 PC1.22: 17 residues within 4Å: Chain 2: Q.6, L.11, Q.12, F.13, R.78 Chain I: I.18, M.21, W.133, L.136, I.206, L.346 Chain Z: P.1, F.2, F.3, V.5 Ligands: PC1.11, CDL.16 11 PLIP interactions: 4 interactions with chain Z, 3 interactions with chain 2, 4 interactions with chain I Hydrophobic interactions: Z:P.1, Z:F.3, Z:F.3, Z:V.5, I:I.18, I:W.133, I:L.136, I:I.206 Hydrogen bonds: 2:L.11, 2:R.78 Salt bridges: 2:R.78

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.14: 15 residues within 4Å: Chain K: L.446, L.449, N.450 Chain M: N.23, W.66 Ligands: CDL.15 Chain a: S.74, V.77, A.78, Y.79 Chain h: L.30, V.37, I.40, E.49, H.69 13 PLIP interactions: 4 interactions with chain K, 3 interactions with chain a, 6 interactions with chain h Hydrophobic interactions: K:L.446, K:L.449, a:V.77, a:A.78, a:Y.79, h:L.30, h:V.37, h:V.37, h:I.40 Hydrogen bonds: K:N.450, K:N.450, h:E.49, h:H.69 CDL.15: 22 residues within 4Å: Chain K: A.357, W.358, L.360, L.364, L.369, P.371, L.442, L.445 Chain M: L.15, I.19, I.22, K.28, Q.116, K.119, Y.120, L.123, I.126, T.127, M.150 Ligands: CDL.14 Chain h: L.22, R.26 23 PLIP interactions: 9 interactions with chain K, 1 interactions with chain h, 13 interactions with chain M Hydrophobic interactions: K:A.357, K:W.358, K:L.364, K:L.369, K:P.371, K:L.442, K:L.445, K:L.445, M:L.15, M:I.19, M:I.22, M:I.22, M:L.123, M:I.126, M:T.127 Hydrogen bonds: K:A.357, M:Q.116, M:Y.120 Salt bridges: h:R.26, M:K.28, M:K.119, M:K.119, M:K.119 CDL.16: 13 residues within 4Å: Chain I: M.11, L.15, I.18 Chain J: T.89, M.90 Chain N: T.151, W.152, I.155, W.159 Chain Z: V.11, L.13 Ligands: PC1.12, PC1.22 6 PLIP interactions: 3 interactions with chain N, 2 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: N:W.159, I:L.15, I:I.18, J:T.89 Hydrogen bonds: N:T.151, N:T.151 CDL.20: 15 residues within 4Å: Chain G: E.44 Chain H: Y.43 Chain V: S.2, A.3, T.4, I.7 Chain W: L.3, V.6, L.7, R.9, G.10, Q.13, Y.23 Chain d: F.3, L.6 9 PLIP interactions: 2 interactions with chain d, 2 interactions with chain V, 1 interactions with chain H, 4 interactions with chain W Hydrophobic interactions: d:F.3, d:L.6, H:Y.43, W:V.6, W:L.7 Hydrogen bonds: V:S.2, V:S.2, W:G.10, W:Q.13

1 x ZN: ZINC ION(Non-covalent)

ZN.18: 4 residues within 4Å: Chain P: C.59, H.68, C.84, C.87 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.59, P:H.68, P:C.84, P:C.87

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.19: 18 residues within 4Å: Chain F: R.178 Chain R: G.25, T.27, G.28, F.29, L.30, R.50, E.52, V.95, G.96, R.97, E.98, F.104, F.110, I.132, H.134, A.169, I.171 16 PLIP interactions: 15 interactions with chain R, 1 interactions with chain F Hydrophobic interactions: R:I.171, R:I.171 Hydrogen bonds: R:L.30, R:R.50, R:R.50, R:V.95, R:V.95, R:G.96, R:E.98, R:E.98 Salt bridges: R:R.50, R:R.97, R:R.97, F:R.178 pi-Stacking: R:F.104 pi-Cation interactions: R:R.50

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

ZMP.21: 14 residues within 4Å: Chain U: K.28, V.31, L.34, W.38, V.62, M.65, F.66, N.69, A.70, V.78, E.88, F.105 Chain X: D.43, S.44 10 PLIP interactions: 1 interactions with chain X, 9 interactions with chain U Hydrogen bonds: X:S.44, U:N.69 Hydrophobic interactions: U:W.38, U:W.38, U:W.38, U:M.65, U:F.66, U:V.78, U:F.105 Salt bridges: U:K.28

1 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.25: 11 residues within 4Å: Chain 7: H.11, Q.12, V.15, H.50, K.51, A.59, T.60, L.63 Chain g: D.43, S.44, L.45 7 PLIP interactions: 3 interactions with chain 7, 4 interactions with chain g Hydrophobic interactions: 7:Q.12 Hydrogen bonds: 7:H.50, g:D.43, g:D.43, g:S.44, g:L.45 Salt bridges: 7:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fiedorczuk, K. et al., Atomic structure of the entire mammalian mitochondrial complex I. Nature (2016)

Release Date

2016-11-23

Peptides

Mitochondrial complex I, 51 kDa subunit: A
Mitochondrial complex I, 24 kDa subunit: B
Mitochondrial complex I, 75 kDa subunit: C
Mitochondrial complex I, 49 kDa subunit: D
Mitochondrial complex I, 30 kDa subunit: E
Mitochondrial complex I, PSST subunit: F
Mitochondrial complex I, TYKY subunit: G
Mitochondrial complex I, ND1 subunit: H
Mitochondrial complex I, ND2 subunit: I
Mitochondrial complex I, ND3 subunit: J
Mitochondrial complex I, ND4 subunit: K
Mitochondrial complex I, ND4L subunit: L
Mitochondrial complex I, ND5 subunit: M
Mitochondrial complex I, ND6 subunit: N
Mitochondrial complex I, 10 kDa subunit: O
Mitochondrial complex I, 13 kDa subunit: P
Mitochondrial complex I, 18 kDa subunit: Q
Mitochondrial complex I, 39 kDa subunit: R
Mitochondrial complex I, B8 subunit: S
Mitochondrial complex I, B13 subunit: T
Mitochondrial complex I, B14 subunit: U
Mitochondrial complex I, B14.5a subunit: V
Mitochondrial complex I, B17.2 subunit: W
Acyl carrier protein: Xg
Mitochondrial complex I, 42 kDa subunit: Y
Mitochondrial complex I, 15 kDa subunit: Z
Mitochondrial complex I, B9 subunit: 0
Mitochondrial complex I, B12 subunit: 1
Mitochondrial complex I, B14.5b subunit: 2
Mitochondrial complex I, B15 subunit: 3
Mitochondrial complex I, B16.6 subunit: 4
Mitochondrial complex I, B17 subunit: 5
Mitochondrial complex I, B18 subunit: 6
Mitochondrial complex I, B22 subunit: 7
Mitochondrial complex I, AGGG subunit: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: 9
Mitochondrial complex I, ESSS subunit: a
Mitochondrial complex I, KFYI subunit: b
Mitochondrial complex I, MNLL subunit: c
Mitochondrial complex I, MWFE subunit: d
Mitochondrial complex I, PDSW subunit: e
Mitochondrial complex I, PGIV subunit: f
Mitochondrial complex I, SGDH subunit: h
Mitochondrial complex I, B14.7 subunit: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
9

H
H

I
N

J
A

K
M

L
K

M
L

N
J

O
a

P
b

Q
c

R
d

S
e

T
f

U
g

V
h

W
i

X
j

g
X

Y
k

Z
l

0
m

1
n

2
o

3
p

4
q

5
r

6
s

7
t

8
u

9
v

a
w

b
x

c
y

d
z

e
Z

f
Y

h
W

i
V

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial complex I, 51 kDa subunit

Mitochondrial complex I, 24 kDa subunit

Mitochondrial complex I, 75 kDa subunit

Mitochondrial complex I, 49 kDa subunit

Mitochondrial complex I, 30 kDa subunit

Mitochondrial complex I, PSST subunit

Mitochondrial complex I, TYKY subunit

Mitochondrial complex I, ND1 subunit

Mitochondrial complex I, ND2 subunit

Mitochondrial complex I, ND3 subunit

Mitochondrial complex I, ND4 subunit

Mitochondrial complex I, ND4L subunit

Mitochondrial complex I, ND5 subunit

Mitochondrial complex I, ND6 subunit

Mitochondrial complex I, 10 kDa subunit

Mitochondrial complex I, 13 kDa subunit

Mitochondrial complex I, 18 kDa subunit

Mitochondrial complex I, 39 kDa subunit

Mitochondrial complex I, B8 subunit

Mitochondrial complex I, B13 subunit

Mitochondrial complex I, B14 subunit

Mitochondrial complex I, B14.5a subunit

Mitochondrial complex I, B17.2 subunit

Acyl carrier protein

Mitochondrial complex I, 42 kDa subunit

Mitochondrial complex I, 15 kDa subunit

Mitochondrial complex I, B9 subunit

Mitochondrial complex I, B12 subunit

Mitochondrial complex I, B14.5b subunit

Mitochondrial complex I, B15 subunit

Mitochondrial complex I, B16.6 subunit

Mitochondrial complex I, B17 subunit

Mitochondrial complex I, B18 subunit

Mitochondrial complex I, B22 subunit

Mitochondrial complex I, AGGG subunit

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

Mitochondrial complex I, ESSS subunit

Mitochondrial complex I, KFYI subunit

Mitochondrial complex I, MNLL subunit

Mitochondrial complex I, MWFE subunit

Mitochondrial complex I, PDSW subunit

Mitochondrial complex I, PGIV subunit

Mitochondrial complex I, SGDH subunit

Mitochondrial complex I, B14.7 subunit

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