SMTL ID : 7eu3.1

Chloroplast NDH complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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

1 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.1: 11 residues within 4Å: Chain D: K.372, G.457, P.458, L.461, F.462, I.465 Chain F: L.70 Chain X: K.41 Chain Y: W.55, Y.56, W.71 8 PLIP interactions: 3 interactions with chain Y, 3 interactions with chain D, 1 interactions with chain X, 1 interactions with chain F Hydrophobic interactions: Y:W.55, Y:Y.56, Y:W.71, D:F.462, D:I.465, X:K.41, F:L.70 Salt bridges: D:K.372

1 x BCR: BETA-CAROTENE(Non-covalent)

BCR.2: 14 residues within 4Å: Chain D: L.90, F.94, F.339, M.376, F.468, P.470, I.472, G.473, I.474 Chain F: G.65, F.66 Chain X: F.29, W.32 Ligands: SQD.4 13 PLIP interactions: 6 interactions with chain D, 4 interactions with chain X, 3 interactions with chain F Hydrophobic interactions: D:L.90, D:F.94, D:F.468, D:P.470, D:I.472, D:I.474, X:F.29, X:F.29, X:F.29, X:W.32, F:F.66, F:F.66, F:F.66

2 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.3: 12 residues within 4Å: Chain D: I.426, I.430, R.437 Chain F: S.215, Q.218, V.222, T.223, Y.712, F.716, T.717, R.721 Chain Y: R.19 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain F Hydrophobic interactions: D:I.426, D:I.426, D:I.430, F:Y.712, F:Y.712, F:F.716, F:F.716 Hydrogen bonds: D:R.437, F:Q.218, F:T.717, F:R.721 SQD.4: 15 residues within 4Å: Chain D: P.371, F.374, T.375, S.378, G.389, M.390 Chain F: L.68, I.69, E.161, G.162, R.165, V.168, Y.169, L.202 Ligands: BCR.2 12 PLIP interactions: 1 interactions with chain D, 11 interactions with chain F Hydrogen bonds: D:T.375, F:E.161, F:R.165, F:R.165 Hydrophobic interactions: F:L.68, F:I.69, F:V.168, F:L.202, F:L.202 Salt bridges: F:R.165, F:R.165, F:R.165

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

SF4.5: 13 residues within 4Å: Chain W: Y.39, N.48, C.49, S.50, G.51, G.52, G.53, E.54, C.55, G.56, T.57, C.58, C.91 1 PLIP interactions: 1 interactions with chain W, Metal complexes: W:C.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, L. et al., Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare. Nature (2022)

Release Date

2021-12-29

Peptides

NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic: A
NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic: B
NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic: C
NAD(P)H-quinone oxidoreductase chain 4, chloroplastic: D
NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic: E
NAD(P)H-quinone oxidoreductase subunit F: F
NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic: G
NAD(P)H-quinone oxidoreductase subunit H, chloroplastic: H
NAD(P)H-quinone oxidoreductase subunit I, chloroplastic: I
NAD(P)H-quinone oxidoreductase subunit J: J
NAD(P)H-quinone oxidoreductase subunit K, chloroplastic: K
NAD(P)H-quinone oxidoreductase subunit L: L
NAD(P)H-quinone oxidoreductase subunit M: M
NAD(P)H-quinone oxidoreductase subunit N: N
Unidentified stromal protein: O
Photosynthetic NDH subunit of subcomplex L1: P
Photosynthetic NDH subunit of subcomplex L2: Q
Photosynthetic NDH subunit of subcomplex L3: R
Photosynthetic NDH subunit of subcomplex L4: S
Photosynthetic NDH subunit of subcomplex L5: T
Photosynthetic NDH subunit of subcomplex B1: U
Photosynthetic NDH subunit of subcomplex B2: V
Photosynthetic NDH subunit of subcomplex B3: W
Photosynthetic NDH subunit of subcomplex B4: X
Photosynthetic NDH subunit of subcomplex B5: Y

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
T

P
1

Q
2

R
3

S
4

T
5

U
6

V
7

W
8

X
9

Y
0

Membrane

We predict this structure to be a membrane protein.
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NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic

NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic

NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic

NAD(P)H-quinone oxidoreductase chain 4, chloroplastic

NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic

NAD(P)H-quinone oxidoreductase subunit F

NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic

NAD(P)H-quinone oxidoreductase subunit H, chloroplastic

NAD(P)H-quinone oxidoreductase subunit I, chloroplastic

NAD(P)H-quinone oxidoreductase subunit J

NAD(P)H-quinone oxidoreductase subunit K, chloroplastic

NAD(P)H-quinone oxidoreductase subunit L

NAD(P)H-quinone oxidoreductase subunit M

NAD(P)H-quinone oxidoreductase subunit N

Unidentified stromal protein

Photosynthetic NDH subunit of subcomplex L1

Photosynthetic NDH subunit of subcomplex L2

Photosynthetic NDH subunit of subcomplex L3

Photosynthetic NDH subunit of subcomplex L4

Photosynthetic NDH subunit of subcomplex L5

Photosynthetic NDH subunit of subcomplex B1

Photosynthetic NDH subunit of subcomplex B2

Photosynthetic NDH subunit of subcomplex B3

Photosynthetic NDH subunit of subcomplex B4

Photosynthetic NDH subunit of subcomplex B5

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