SMTL ID : 8b9z.1

Drosophila melanogaster complex I in the Active state (Dm1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.28 Å

Oligo State

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

Ligands

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

PC1.1: 9 residues within 4Å: Chain A: H.106, N.109, Q.110 Chain J: K.161 Chain N: S.5, L.9 Chain O: I.31, K.34 Ligands: 3PE.2 5 PLIP interactions: 1 interactions with chain N, 1 interactions with chain A, 2 interactions with chain O, 1 interactions with chain J Hydrogen bonds: N:S.5, A:Q.110 Hydrophobic interactions: O:I.31 Salt bridges: O:K.34, J:K.161 PC1.18: 23 residues within 4Å: Chain H: L.76, S.77, I.80, F.84, L.118, Y.121, T.122, M.124, V.125, W.128 Chain J: L.28, M.62, L.65, F.66, V.69, F.78, N.79, L.80 Chain K: L.33 Chain P: R.204, Y.350 Ligands: 3PE.19, 3PE.20 16 PLIP interactions: 8 interactions with chain H, 1 interactions with chain K, 7 interactions with chain J Hydrophobic interactions: H:I.80, H:F.84, H:L.118, H:Y.121, H:T.122, H:V.125, H:W.128, K:L.33, J:L.28, J:L.28, J:L.65, J:F.66, J:V.69, J:F.78 Hydrogen bonds: H:S.77, J:N.79 PC1.39: 13 residues within 4Å: Chain 4: A.53, Y.54 Chain 6: Y.109, R.119, G.122, W.123 Chain L: W.39, M.51, L.115 Chain M: P.359, I.436, L.437 Ligands: CDL.37 9 PLIP interactions: 2 interactions with chain 6, 4 interactions with chain L, 3 interactions with chain M Hydrogen bonds: 6:Y.109, L:W.39 Salt bridges: 6:R.119 Hydrophobic interactions: L:W.39, L:W.39, L:L.115, M:P.359, M:I.436, M:L.437

16 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.2: 12 residues within 4Å: Chain 0: L.2, A.6, E.9, I.10, I.13, S.17 Chain A: Y.105, W.108, N.109, G.111, N.114 Ligands: PC1.1 Ligand excluded by PLIP 3PE.3: 12 residues within 4Å: Chain A: L.25 Chain B: L.36, L.40, L.176, W.179, K.182 Chain H: A.59, I.60, F.63 Chain P: P.296 Ligands: UQ9.14, CDL.28 Ligand excluded by PLIP 3PE.5: 10 residues within 4Å: Chain B: Y.18, L.39, W.42, K.45 Chain H: K.46, G.48 Ligands: CDL.6, UQ9.14 Chain e: Y.25, D.28 Ligand excluded by PLIP 3PE.15: 24 residues within 4Å: Chain 0: A.18, L.19 Chain D: R.233, I.234, Q.237 Chain H: L.190, V.193, S.194, L.197, F.205, W.272, L.277, F.280, L.288, C.292, F.293, F.296, Y.300 Chain I: T.34, M.35, F.37, L.40 Chain Y: I.32, Y.35 Ligand excluded by PLIP 3PE.19: 21 residues within 4Å: Chain A: M.1, S.3, I.4, I.5, A.8, L.9 Chain H: F.87, F.91, Y.103, F.105, N.106 Chain J: L.9, I.35, F.36, L.39, F.48, S.51, Y.52, F.55 Chain Y: W.145 Ligands: PC1.18 Ligand excluded by PLIP 3PE.20: 14 residues within 4Å: Chain J: N.19, M.20, I.21, H.22, A.25, T.29, M.77, F.78, N.79, L.80, S.81, L.84, T.85 Ligands: PC1.18 Ligand excluded by PLIP 3PE.21: 12 residues within 4Å: Chain 6: K.130 Chain L: L.19, S.20, L.23, L.24, Y.27, F.28, Y.35, F.55 Chain d: A.9, V.12, L.13 Ligand excluded by PLIP 3PE.22: 20 residues within 4Å: Chain 9: E.56, E.86, D.87, R.88, S.90, Q.91 Chain L: N.138, M.141, L.142, L.145, I.149, S.506, T.507, I.511, P.514, L.515 Chain M: L.265, S.385, F.386, F.389 Ligand excluded by PLIP 3PE.23: 13 residues within 4Å: Chain L: N.265, F.266, F.386, L.390, S.393, G.468, F.471, I.475, S.478, F.482, N.484, K.485, S.486 Ligand excluded by PLIP 3PE.24: 15 residues within 4Å: Chain L: F.533, G.535, Q.536, L.538, Y.539, L.542 Chain M: Q.138, L.141, Y.142, F.145, Y.146, L.149 Chain N: M.280, I.284, F.287 Ligand excluded by PLIP 3PE.25: 15 residues within 4Å: Chain M: L.149, P.153, Y.160, Y.180, L.182, L.183, C.186 Chain N: Y.272, F.273, T.276 Chain X: G.128, W.129, F.131 Ligands: 3PE.33, 3PE.35 Ligand excluded by PLIP 3PE.32: 13 residues within 4Å: Chain 1: L.21, S.22, W.25, N.26 Chain M: F.6, L.9, Y.50, F.51, L.102 Chain N: F.332 Chain W: W.172, L.173, E.174 Ligand excluded by PLIP 3PE.33: 14 residues within 4Å: Chain X: Y.24, A.28, L.60, M.63, A.110, L.114, A.117, I.120, K.121, E.130, F.131, F.132 Ligands: 3PE.25, 3PE.34 Ligand excluded by PLIP 3PE.34: 11 residues within 4Å: Chain X: K.4, Y.5, Y.6, Y.24, F.67, Y.86, L.114, A.117, G.118, K.121 Ligands: 3PE.33 Ligand excluded by PLIP 3PE.35: 12 residues within 4Å: Chain M: L.182, F.185, Y.245 Chain X: D.82, K.83, I.84, L.87, I.116, V.119, I.120, M.123 Ligands: 3PE.25 Ligand excluded by PLIP 3PE.36: 12 residues within 4Å: Chain 1: V.32, I.39, F.40, W.43, V.49 Chain M: F.16, N.87, L.91 Chain N: S.233, I.235, T.239, F.325 Ligand excluded by PLIP

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

SF4.4: 12 residues within 4Å: Chain B: A.56, C.57, C.58, G.93, T.94, G.120, S.121, C.122, C.152, P.153 Chain D: R.105, H.190 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.57, B:C.58, B:C.122, B:C.152 SF4.9: 13 residues within 4Å: Chain F: I.187, P.205, C.361, G.362, Q.363, C.364, C.367, R.368, T.405, I.406, C.407, L.409, G.410 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.361, F:C.364, F:C.367, F:C.407 SF4.10: 11 residues within 4Å: Chain D: M.342 Chain G: H.134, D.137, C.138, C.141, G.144, C.147, L.149, Q.150, V.242, G.243 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.134, G:C.138, G:C.141, G:C.147 SF4.11: 12 residues within 4Å: Chain G: M.187, C.190, I.191, H.192, C.193, T.194, R.195, C.196, I.220, C.240, V.242, A.244 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.190, G:C.193, G:C.196, G:C.240 SF4.16: 12 residues within 4Å: Chain I: H.75, C.97, P.98, I.102, C.126, I.127, Y.128, C.129, G.130, F.131, C.132, E.143 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.143 Metal complexes: I:C.97, I:C.126, I:C.129, I:C.132 SF4.17: 11 residues within 4Å: Chain I: C.87, I.88, A.89, C.90, K.91, C.93, I.104, Y.119, C.136, A.140, I.141 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.87, I:C.90, I:C.93, I:C.136

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.6: 18 residues within 4Å: Chain B: K.15, G.17, Y.18, S.19, T.23, W.31, R.35, L.36, D.38, L.39 Chain H: L.49, P.53 Ligands: 3PE.5, UQ9.14 Chain e: Y.21, L.22, Y.25, N.66 13 PLIP interactions: 8 interactions with chain B, 2 interactions with chain e, 3 interactions with chain H Hydrophobic interactions: B:W.31, B:R.35, B:D.38, B:L.39, H:L.49, H:P.53, H:P.53 Hydrogen bonds: B:Y.18, B:S.19, e:Y.21, e:N.66 Salt bridges: B:K.15, B:R.35 CDL.28: 11 residues within 4Å: Chain A: I.24, L.25, K.28 Chain H: Y.69 Chain P: H.197, I.198, W.199, C.295, G.297, T.298 Ligands: 3PE.3 10 PLIP interactions: 5 interactions with chain P, 5 interactions with chain A Hydrogen bonds: P:G.297, P:T.298, P:T.298, P:G.301 Salt bridges: P:H.197, A:K.28, A:K.28 Hydrophobic interactions: A:I.24, A:I.24, A:L.25 CDL.37: 23 residues within 4Å: Chain 4: V.46, S.49, F.50, Y.54 Chain 5: V.29, T.33, V.36, L.37, N.40, P.45, H.65 Chain 6: Y.104, A.105, Y.108, Y.109, F.110, N.113 Ligands: PC1.39 Chain d: P.19, I.20, F.23, R.24, V.28 21 PLIP interactions: 9 interactions with chain 6, 5 interactions with chain d, 7 interactions with chain 5 Hydrophobic interactions: 6:Y.104, 6:A.105, 6:Y.108, 6:Y.109, 6:Y.109, 6:F.110, d:P.19, d:I.20, d:F.23, d:F.23, 5:V.29, 5:T.33, 5:V.36, 5:V.36, 5:L.37 Hydrogen bonds: 6:Y.108, 6:N.113, 6:N.113, 5:H.65 Salt bridges: d:R.24, 5:H.65 CDL.38: 19 residues within 4Å: Chain 5: R.11, W.14, K.18 Chain L: N.88, R.89, M.92, L.93, M.96, G.119, C.126 Chain M: L.337, P.341, T.344, L.345, W.346, F.348, L.349, Y.399, W.429 15 PLIP interactions: 4 interactions with chain 5, 3 interactions with chain L, 8 interactions with chain M Hydrophobic interactions: 5:W.14, L:M.92, M:L.345, M:W.346, M:F.348, M:F.348, M:F.348, M:F.348, M:L.349, M:W.429 Salt bridges: 5:R.11, 5:R.11, 5:K.18, L:R.89, L:R.89

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

FES.7: 11 residues within 4Å: Chain E: C.100, T.102, T.103, P.104, C.105, C.141, L.142, G.143, A.144, C.145, M.150 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.100, E:C.105, E:C.141, E:C.145 FES.12: 9 residues within 4Å: Chain G: R.72, F.73, C.74, Y.75, G.83, C.85, R.86, C.88, C.102 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.74, G:C.85, G:C.88, G:C.102

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 20 residues within 4Å: Chain F: G.69, R.70, G.71, G.72, A.73, K.80, N.98, D.100, E.101, G.102, Y.186, G.189, E.190, E.191, V.224, T.225, N.226, T.229, A.408, L.409 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:Y.186, F:E.190, F:A.408, F:L.409 Hydrogen bonds: F:R.70, F:G.71, F:G.72, F:A.73, F:N.98, F:D.100, F:G.102, F:G.189, F:E.191, F:N.226, F:T.229 Salt bridges: F:K.80

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 5 residues within 4Å: Chain G: Q.143, I.237, C.240, V.242, L.245 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.143, G:V.242

1 x UQ9: Ubiquinone-9(Non-covalent)

UQ9.14: 21 residues within 4Å: Chain B: L.39, W.49, T.52, F.79, R.80 Chain D: F.168 Chain H: A.25, T.28, R.32, P.55, F.56, D.58, A.59, I.60, L.62, F.231, M.232, R.274 Ligands: 3PE.3, 3PE.5, CDL.6 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: H:A.25, H:T.28, H:F.56, H:F.56, H:A.59, H:I.60, H:F.231, H:F.231, H:F.231, H:F.231, B:W.49

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.26: 19 residues within 4Å: Chain O: I.52, A.53, A.54, G.55, K.56, S.57, F.108, C.109, F.120, Q.121, R.128, E.149, R.150, D.155, F.158, M.162, R.210, E.215, F.221 21 PLIP interactions: 21 interactions with chain O Hydrogen bonds: O:A.53, O:A.54, O:G.55, O:G.55, O:K.56, O:S.57, O:Q.121, O:Q.121, O:Q.121, O:R.128, O:E.215, O:E.215 Salt bridges: O:K.56, O:K.56, O:K.56, O:R.150, O:R.210, O:R.210, O:R.210 pi-Stacking: O:F.158, O:F.158

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

NDP.27: 21 residues within 4Å: Chain B: K.182 Chain P: G.31, T.33, G.34, F.35, V.36, R.56, Y.79, L.81, L.100, V.101, G.102, R.103, F.110, V.115, L.138, W.158, K.162, I.184, R.190, R.310 23 PLIP interactions: 22 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:W.158, P:I.184 Hydrogen bonds: P:G.31, P:T.33, P:T.33, P:G.34, P:F.35, P:V.36, P:R.56, P:V.101, P:G.102, P:K.162, P:I.184, P:I.184, P:R.310 Salt bridges: P:R.56, P:R.103, P:R.103, P:R.190, P:R.190, B:K.182 pi-Cation interactions: P:R.56, P:R.56

1 x ZN: ZINC ION(Non-covalent)

ZN.29: 5 residues within 4Å: Chain R: C.55, G.57, H.64, C.79, C.82 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.55, R:H.64, R:C.79, R:C.82

2 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate(Covalent)

EHZ.30: 19 residues within 4Å: Chain S: S.41 Chain V: R.17, A.20, L.21, L.23, W.27, I.34, V.35, I.40, C.47, E.54, F.55, H.58, R.59, L.70, G.74, I.91, Y.94, W.95 12 PLIP interactions: 12 interactions with chain V Hydrophobic interactions: V:L.23, V:W.27, V:W.27, V:I.34, V:V.35, V:I.40, V:F.55, V:Y.94 Hydrogen bonds: V:R.17, V:R.59, V:Y.94, V:Y.94 EHZ.31: 19 residues within 4Å: Chain L: L.487 Chain T: D.40, S.41, L.42 Chain b: H.10, K.11, V.14, L.42, R.45, F.46, N.49, R.50, K.52, L.54, L.60, G.64, E.67, L.68, T.71 11 PLIP interactions: 1 interactions with chain L, 2 interactions with chain T, 8 interactions with chain b Hydrophobic interactions: L:L.487, b:K.11, b:L.68 Hydrogen bonds: T:S.41, T:L.42, b:R.45, b:N.49, b:N.49, b:R.50 Salt bridges: b:K.11, b:R.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agip, A.A. et al., Cryo-EM structures of mitochondrial respiratory complex I from Drosophila melanogaster. Elife (2023)

Release Date

2023-01-18

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
LD31474p: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: C
Complex I-49kD: D
NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: F
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH dehydrogenase (ubiquinone) 23 kDa subunit: I
NADH-ubiquinone oxidoreductase chain 6: J
NADH-ubiquinone oxidoreductase chain 4L: K
NADH-ubiquinone oxidoreductase chain 5: L
NADH-ubiquinone oxidoreductase chain 4: M
NADH-ubiquinone oxidoreductase chain 2: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: O
NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: R
Acyl carrier protein, mitochondrial: ST
NADH dehydrogenase (Ubiquinone) 13 kDa B subunit: U
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: Z
RH45008p: 0
NADH dehydrogenase [ubiquinone] 1 subunit C2: 1
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 3
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 4
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: 6
GEO11417p1: 7
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: d
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: e
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: f
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: g

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
T

T
U

U
V

V
W

W
X

X
Y

Y
Z

Z
a

0
b

1
d

2
e

3
f

4
g

5
h

6
i

7
j

8
k

9
l

a
m

b
n

c
o

d
p

e
q

f
r

g
s

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 3

LD31474p

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

Complex I-49kD

NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase (ubiquinone) 23 kDa subunit

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

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

NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

Acyl carrier protein, mitochondrial

NADH dehydrogenase (Ubiquinone) 13 kDa B subunit

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

RH45008p

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

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

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

GEO11417p1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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