SMTL ID : 5o31.1

Mitochondrial complex I in the deactive state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.13 Å

Oligo State

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

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.105, H.190 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D, Metal complexes: B:C.54, B:C.55, B:C.119, B:C.149 pi-Cation interactions: D:H.190 SF4.4: 11 residues within 4Å: Chain F: P.223, C.379, G.380, Q.381, C.382, C.385, T.423, I.424, C.425, L.427, G.428 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.379, F:C.382, F:C.385, F:C.425 SF4.5: 11 residues within 4Å: Chain H: H.65, C.87, P.88, I.111, C.116, I.117, Y.118, C.119, G.120, F.121, C.122 5 PLIP interactions: 5 interactions with chain H, Salt bridges: H:E.133 Metal complexes: H:C.87, H:C.116, H:C.119, H:C.122 SF4.6: 13 residues within 4Å: Chain H: C.77, I.78, A.79, C.80, K.81, L.82, C.83, Y.109, C.126, P.127, V.128, A.130, I.131 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.77, H:C.80, H:C.83, H:C.126 SF4.8: 11 residues within 4Å: Chain 8: H.101, D.104, C.105, C.108, Q.110, C.114, Q.117, R.152, V.205, G.206 Chain D: M.342 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:H.101, 8:C.105, 8:C.108, 8:C.114 SF4.9: 12 residues within 4Å: Chain 8: M.150, C.153, I.154, Q.155, C.156, T.157, R.158, C.159, C.203, V.205, A.207, L.208 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:C.153, 8:C.156, 8:C.159, 8:C.203

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, G.146, A.147, C.148 Chain F: P.122 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.103, E:C.108, E:C.144, E:C.148 FES.10: 11 residues within 4Å: Chain 8: R.39, F.40, 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 8, Metal complexes: 8:C.41, 8:C.52, 8:C.55, 8:C.69

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 18 residues within 4Å: Chain F: G.87, R.88, G.89, G.90, A.91, N.116, D.118, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:Y.204, F:A.426 Hydrogen bonds: F:G.89, F:D.118, F:G.207, F:N.244

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

NAP.7: 19 residues within 4Å: Chain O: X.24, X.25, X.26, X.27, X.28, X.29, X.49, X.50, X.74, X.93, X.94, X.95, X.96, X.108, X.131, X.133, X.167, X.168, X.170 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain b: C.59, H.68, C.84, C.87 4 PLIP interactions: 4 interactions with chain b Metal complexes: b:C.59, b:H.68, b:C.84, b:C.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaza, J.N. et al., Structure of the Deactive State of Mammalian Respiratory Complex I. Structure (2018)

Release Date

2018-01-17

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 chain 1: G
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: H
NADH-ubiquinone oxidoreductase chain 6: I
NADH-ubiquinone oxidoreductase chain 4L: J
NADH-ubiquinone oxidoreductase chain 5: K
NADH-ubiquinone oxidoreductase chain 4: L
NADH-ubiquinone oxidoreductase chain 2: M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: P
Acyl carrier protein, mitochondrial: QR
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: S
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: T
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: U
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: W
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: X
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: Y
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: Z
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 0
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: 1
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2: 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: 3
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8: 4
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: 6
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: 7
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: 8
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: 9
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: a
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: b
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: d
NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2: e
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: f
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: g
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: h
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
O

O
P

P
S

Q
T

R
U

S
V

T
W

U
Y

V
a

W
b

X
c

Y
e

Z
f

0
g

1
i

2
j

3
k

4
l

5
o

6
p

7
q

8
G

9
s

a
Q

b
R

c
r

d
h

e
d

f
X

g
m

h
n

i
Z

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 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, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9

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 11

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 subunit C1, mitochondrial

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

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

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