SMTL ID : 5ldw.1

Structure of mammalian respiratory Complex I, class1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.27 Å

Oligo State

hetero-oligomer

Ligands

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

SF4.1: 12 residues within 4Å: Chain B: A.53, C.54, C.55, G.90, T.91, G.117, S.118, C.119, C.149, P.150 Chain D: R.104, H.189 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.54, B:C.55, B:C.119, B:C.149 SF4.4: 9 residues within 4Å: Chain F: P.203, C.359, Q.361, C.362, C.365, T.403, C.405, L.407, G.408 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.359, F:C.362, F:C.365, F:C.405 SF4.5: 10 residues within 4Å: Chain G: H.94, D.97, C.98, C.101, Q.103, C.107, L.109, Q.110, V.198, G.199 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.97 Metal complexes: G:H.94, G:C.98, G:C.101, G:C.107 SF4.6: 7 residues within 4Å: Chain G: C.146, I.147, C.149, R.151, C.152, V.176, C.196 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.146, G:C.149, G:C.152, G:C.196 SF4.8: 11 residues within 4Å: Chain I: H.65, C.87, P.88, A.89, C.116, I.117, Y.118, C.119, G.120, F.121, C.122 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.133 Metal complexes: I:C.87, I:C.116, I:C.119, I:C.122 SF4.9: 12 residues within 4Å: Chain I: C.77, I.78, A.79, C.80, L.82, C.83, Y.109, C.126, P.127, V.128, A.130, I.131 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.77, I:C.80, I:C.83, I:C.126

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

FES.2: 10 residues within 4Å: Chain E: C.103, T.105, P.107, C.108, C.144, L.145, A.147, C.148, M.153 Chain F: P.102 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.103, E:C.108, E:C.144, E:C.148 FES.7: 8 residues within 4Å: Chain G: R.32, F.33, C.34, A.42, G.43, C.45, C.48, C.62 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.34, G:C.45, G:C.48, G:C.62

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 15 residues within 4Å: Chain F: R.68, G.69, G.70, A.71, N.96, D.98, G.100, C.186, G.187, E.188, E.189, V.222, A.223, N.224, A.406 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:A.406 Hydrogen bonds: F:G.69, F:G.70, F:D.98, F:G.187, F:N.224

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.10: 17 residues within 4Å: Chain P: X.24, X.25, X.27, X.28, X.29, X.49, X.50, X.74, X.95, X.96, X.108, X.131, X.167, X.168, X.169, X.170, X.177 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain R: C.55, H.64, C.80, C.83 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.55, R:H.64, R:C.80, R:C.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, J. et al., Structure of mammalian respiratory complex I. Nature (2016)

Release Date

2016-09-07

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: F
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: 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, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, NDUFA9: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4: Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, NDUFS6,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: S
Acyl carrier protein, mitochondrial: TU
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, NDUFA8: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: 0
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3, NDUFA3: 1
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 2
NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2: 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 4
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, NDUFB5: 7
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6, NDUFB6: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, NDUFB4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, NDUFB4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9, NDUFB9: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: e
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10: f
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: g
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7: h
NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3: i

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
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

2
c

3
d

4
e

5
f

6
g

7
h

8
i

9
j

a
k

b
l

c
m

d
n

e
o

f
p

g
q

h
r

i
s

Membrane

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial

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, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, NDUFA9

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, NDUFS6,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, NDUFA8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3, NDUFA3

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2

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 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, NDUFB5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6, NDUFB6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, NDUFB4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, NDUFB4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9, NDUFB9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7

NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3

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