SMTL ID : 9cwt.1

Human kidney respiratory complex I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.205, P.223, S.378, 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 A, Metal complexes: A:C.379, A:C.382, A:C.385, A:C.425 SF4.3: 10 residues within 4Å: Chain B: C.111, I.112, C.114, L.116, I.128, Y.143, C.160, V.162, A.164, I.165 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.111, B:C.114, B:Y.143, B:C.160 SF4.4: 13 residues within 4Å: Chain B: H.99, C.117, C.121, I.126, I.145, C.150, Y.152, C.153, G.154, F.155, C.156, I.165, E.167 7 PLIP interactions: 7 interactions with chain B, Salt bridges: B:E.167, B:E.167 Metal complexes: B:H.99, B:C.121, B:C.150, B:C.153, B:C.156 SF4.5: 13 residues within 4Å: Chain C: A.87, C.88, C.89, G.124, T.125, G.151, S.152, C.153, G.182, C.183, P.184 Chain P: R.138, H.223 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.88, C:C.89, C:C.153, C:C.183 SF4.8: 12 residues within 4Å: Chain L: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, Q.140, V.228 Chain P: M.375, I.379 3 PLIP interactions: 3 interactions with chain L, Metal complexes: L:H.124, L:C.128, L:C.137 SF4.9: 11 residues within 4Å: Chain L: C.176, I.177, C.179, T.180, R.181, C.182, V.206, C.226, V.228, A.230, L.231 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.176, L:C.179, L:C.182, L:C.226

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain A: G.87, R.88, G.89, A.91, N.116, D.118, E.119, D.127, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.116, A:N.244 Hydrogen bonds: A:R.88, A:G.89, A:F.93, A:N.116, A:G.207, A:G.207, A:E.209, A:N.244, A:A.426

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

ZMP.6: 18 residues within 4Å: Chain D: M.25, K.29, V.32, L.35, W.39, V.63, M.66, F.67, M.68, N.70, A.71, V.73, V.79, L.82, V.83, G.86 Chain F: S.112, L.113 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:K.29, D:W.39, D:W.39, D:W.39, D:V.63, D:F.67 Hydrogen bonds: F:S.112

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

NDP.7: 24 residues within 4Å: Chain I: G.60, A.61, T.62, G.63, F.64, L.65, R.85, C.86, L.129, I.130, G.131, R.132, F.139, V.144, F.145, V.167, S.168, H.169, Y.180, K.184, P.203, D.205, I.206, R.212 24 PLIP interactions: 24 interactions with chain I Hydrophobic interactions: I:P.203, I:I.206 Hydrogen bonds: I:G.60, I:T.62, I:T.62, I:G.63, I:F.64, I:L.65, I:R.85, I:C.86, I:L.129, I:G.131, I:R.132, I:D.205, I:I.206, I:I.206, I:R.212 Salt bridges: I:R.85, I:R.132, I:R.132, I:R.212, I:R.212 pi-Cation interactions: I:R.85, I:R.132

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

FES.10: 11 residues within 4Å: Chain L: R.62, F.63, C.64, Y.65, A.72, G.73, N.74, C.75, M.77, C.78, C.92 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.64, L:C.75, L:C.78, L:C.92 FES.11: 9 residues within 4Å: Chain N: C.135, T.137, C.140, C.176, L.177, G.178, A.179, C.180, M.185 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.135, N:C.140, N:C.176, N:C.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Human kidney respiratory complex I. To Be Published

Release Date

2025-08-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

V
X

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
O

O
P

P
Q

Q
S

R
T

S
U

T
V

U
W

W
Y

X
Z

Y
a

Z
b

0
c

1
d

2
e

3
f

4
g

5
h

6
j

7
k

8
l

9
m

a
n

b
o

c
p

d
r

e
s

f
u

g
v

h
D

i
i

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

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 7

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

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

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

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

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

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

Unknow peptide

NADH-ubiquinone oxidoreductase chain 2

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