SMTL ID : 8ba0.1

Drosophila melanogaster complex I in the Twisted state (Dm2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.68 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

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

SF4.1: 10 residues within 4Å: Chain B: C.57, C.58, G.93, G.120, S.121, C.122, C.152, P.153 Chain D: R.103, H.188 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.57, B:C.58, B:C.122, B:C.152 SF4.6: 12 residues within 4Å: Chain F: I.187, P.205, S.360, C.361, G.362, Q.363, C.364, C.367, T.405, I.406, C.407, L.409 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.361, F:C.364, F:C.367, F:C.407 SF4.7: 11 residues within 4Å: Chain D: M.340 Chain G: H.134, D.137, C.138, C.141, Q.143, G.144, C.147, 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 SF4.8: 11 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 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.190, G:C.193, G:C.196, G:C.240 SF4.10: 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 6 PLIP interactions: 6 interactions with chain I, Salt bridges: I:E.143, I:E.143 Metal complexes: I:C.97, I:C.126, I:C.129, I:C.132 SF4.11: 13 residues within 4Å: Chain I: C.87, I.88, A.89, C.90, K.91, C.93, I.104, Y.119, C.136, P.137, V.138, 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

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

3PE.2: 9 residues within 4Å: Chain B: Y.18, L.39, W.42, K.45 Chain H: K.46, G.48 Chain e: Y.27, D.30, M.69 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain e Hydrophobic interactions: B:L.39, B:W.42 Hydrogen bonds: B:Y.18, e:D.30 Salt bridges: B:K.45 3PE.3: 8 residues within 4Å: Chain A: L.25, K.27 Chain B: T.175, L.176, W.179, K.182 Chain P: P.296 Ligands: CDL.16 8 PLIP interactions: 6 interactions with chain B, 1 interactions with chain P, 1 interactions with chain A Hydrophobic interactions: B:L.176, B:W.179, B:W.179, P:P.296, A:K.27 Hydrogen bonds: B:T.175, B:T.175 Salt bridges: B:K.182 3PE.12: 18 residues within 4Å: Chain 9: E.85, R.87, W.88, S.89 Chain L: N.138, M.141, L.142, L.145, S.146, I.149, F.202, S.506, T.507, M.510, I.511, P.514 Chain M: F.389, F.390 9 PLIP interactions: 3 interactions with chain M, 2 interactions with chain 9, 4 interactions with chain L Hydrophobic interactions: M:F.389, M:F.390, M:F.390, L:L.142, L:I.149, L:F.202 Hydrogen bonds: 9:E.85, 9:S.89, L:N.138 3PE.20: 6 residues within 4Å: Chain X: Y.6, K.121, E.130, F.131, F.132 Ligands: 3PE.21 5 PLIP interactions: 5 interactions with chain X Hydrophobic interactions: X:F.131 Hydrogen bonds: X:E.130, X:F.132 Salt bridges: X:K.121, X:K.121 3PE.21: 9 residues within 4Å: Chain X: K.4, Y.5, Y.6, T.21, Y.24, F.67, Y.86, K.121 Ligands: 3PE.20 8 PLIP interactions: 8 interactions with chain X Hydrophobic interactions: X:Y.5, X:F.67, X:Y.86, X:K.121 Hydrogen bonds: X:K.4, X:K.4 Salt bridges: X:K.121, X:K.121 3PE.22: 12 residues within 4Å: Chain M: Y.160, K.164, Y.180, L.182, L.183 Chain N: N.270, Y.272, F.273 Chain X: Q.127, G.128, W.129, F.131 13 PLIP interactions: 3 interactions with chain X, 6 interactions with chain M, 4 interactions with chain N Hydrophobic interactions: X:W.129, X:F.131, M:Y.160, M:L.182, M:L.182, N:Y.272, N:F.273 Hydrogen bonds: X:Q.127, M:Y.160, M:Y.160, N:N.270, N:Y.272 Salt bridges: M:K.164

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

FES.4: 11 residues within 4Å: Chain E: C.100, T.102, T.103, C.105, E.140, 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.9: 10 residues within 4Å: Chain G: R.72, F.73, C.74, Y.75, G.83, N.84, 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.5: 22 residues within 4Å: Chain F: G.69, R.70, G.71, F.75, S.77, K.80, N.98, D.100, E.101, G.102, E.103, Y.186, I.187, G.189, E.190, E.191, V.224, T.225, N.226, T.229, A.408, L.409 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:Y.186, F:I.187, F:A.408, F:L.409 Hydrogen bonds: F:G.69, F:G.71, F:N.98, F:D.100, F:G.102, F:E.103, F:G.189, F:E.191, F:E.191, F:N.226 Salt bridges: F:K.80

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.13: 17 residues within 4Å: Chain 5: R.11, W.14, K.18 Chain L: H.86, R.89, M.92, L.93, M.96, V.123, C.126 Chain M: L.337, P.341, S.342, T.344, L.345, F.348, Y.399 14 PLIP interactions: 6 interactions with chain L, 3 interactions with chain 5, 5 interactions with chain M Hydrophobic interactions: L:M.92, L:L.93, L:V.123, M:L.337, M:T.344, M:L.345, M:F.348, M:F.348 Hydrogen bonds: L:H.86, 5:R.11, 5:R.11 Salt bridges: L:R.89, L:R.89, 5:K.18 CDL.16: 12 residues within 4Å: Chain A: F.20, S.23, I.24, K.28 Chain P: H.197, W.199, C.295, P.296, T.298, I.300, G.301 Ligands: 3PE.3 9 PLIP interactions: 5 interactions with chain P, 4 interactions with chain A Hydrophobic interactions: P:W.199, P:I.300, A:F.20, A:I.24 Hydrogen bonds: P:T.298, P:G.301 Salt bridges: P:H.197, A:K.28, A:K.28

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

DGT.14: 18 residues within 4Å: Chain O: I.52, A.53, A.54, G.55, K.56, S.57, A.74, V.105, F.108, F.120, M.124, R.128, E.149, D.155, F.158, M.162, R.210, E.215 14 PLIP interactions: 14 interactions with chain O Hydrophobic interactions: O:I.52 Hydrogen bonds: O:A.53, O:A.54, O:G.55, O:S.57, O:R.128, O:E.149, O:E.215 Salt bridges: O:K.56, O:K.56, O:R.210, O:R.210 pi-Stacking: O:F.158 pi-Cation interactions: O:F.108

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

NDP.15: 26 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, D.104, F.110, V.115, H.116, L.138, S.140, W.158, K.162, P.181, D.183, I.184, R.190, R.310 25 PLIP interactions: 24 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:W.158, P:I.184 Hydrogen bonds: P:T.33, P:T.33, P:T.33, P:F.35, P:V.36, P:R.56, P:G.57, P:L.100, P:G.102, P:R.103, P:H.116, P:K.162, P:I.184, P:R.310, 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.17: 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.18: 20 residues within 4Å: Chain S: D.107, S.108 Chain V: R.17, L.23, W.27, I.31, I.34, V.35, I.40, C.47, L.51, E.54, F.55, H.58, R.59, I.67, G.74, E.77, Y.94, W.95 16 PLIP interactions: 15 interactions with chain V, 1 interactions with chain S Hydrophobic interactions: V:W.27, V:W.27, V:W.27, V:W.27, V:I.31, V:I.34, V:V.35, V:I.40, V:Y.94, V:W.95 Hydrogen bonds: V:W.27, V:E.54, V:E.77, S:S.108 Salt bridges: V:R.17, V:R.59 EHZ.19: 20 residues within 4Å: Chain T: D.107, S.108, L.109 Chain b: H.10, V.14, A.21, N.24, L.25, W.28, Y.29, L.42, R.45, F.46, N.49, R.50, L.60, G.64, E.67, L.68, T.71 15 PLIP interactions: 13 interactions with chain b, 2 interactions with chain T Hydrophobic interactions: b:A.21, b:N.24, b:L.25, b:W.28, b:Y.29, b:L.42, b:L.60, b:L.60, b:E.67, b:L.68, T:L.109 Hydrogen bonds: b:N.49, b:R.50, T:S.108 Salt bridges: 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.
Show / Hide

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

Related Entries With Identical Sequence