SMTL ID : 6tjv.1

Structure of the NDH-1MS complex from Thermosynechococcus elongatus

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-mer

Ligands

2 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)(Covalent)

DGD.1: 23 residues within 4Å: Chain A: D.6, L.7, Q.8, W.29, L.32, P.33, L.35, M.36, M.37, V.40, V.43, G.44, F.119, N.122, L.123, L.124, S.126, V.266, L.315 Chain C: Y.21 Chain L: Y.20, T.52 Ligands: DGD.13 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.32, A:L.35, A:L.35, A:V.40, A:V.43, A:F.119, A:F.119, A:L.123, A:V.266, A:L.315, A:L.315 Hydrogen bonds: A:D.6, A:L.7, A:Q.8, A:S.126, C:Y.21 DGD.13: 19 residues within 4Å: Chain A: D.6, L.7, V.43, Q.121, N.122, L.123, W.280, Q.303, F.306, A.307, V.308 Chain L: L.16, A.17, L.19, Y.20, F.53, F.54, P.56 Ligands: DGD.1 15 PLIP interactions: 9 interactions with chain L, 6 interactions with chain A Hydrophobic interactions: L:L.16, L:L.16, L:A.17, L:L.19, L:Y.20, L:Y.20, L:Y.20, L:F.54, L:P.56, A:V.43, A:L.123, A:V.308 Hydrogen bonds: A:D.6, A:Q.121, A:N.122

2 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.2: 15 residues within 4Å: Chain A: L.27, L.30, L.138 Chain C: F.14, S.17, G.18, Y.19, E.20, F.22, L.26 Chain G: L.3, T.7, G.48, L.52, I.63 12 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C, 4 interactions with chain G Hydrophobic interactions: A:L.27, A:L.30, A:L.138, C:E.20, C:F.22, C:F.22, C:L.26, G:L.3, G:T.7, G:L.52, G:I.63 Hydrogen bonds: C:G.18 PGT.4: 14 residues within 4Å: Chain B: L.294, L.416, Y.423, K.430 Chain D: Q.160, V.163, I.167, Y.168, P.226 Chain F: T.564, G.565, G.569, T.572, L.573 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 3 interactions with chain D Hydrogen bonds: B:K.430, B:K.430 Hydrophobic interactions: F:T.572, D:I.167, D:I.167, D:Y.168

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

SQD.3: 21 residues within 4Å: Chain D: P.367, L.368, L.371, P.372, T.373, T.374, A.376, R.447, V.448, K.453, L.457 Chain F: M.20, L.24, S.27, G.29, I.30, R.32, A.124, L.125, L.128 Chain P: R.357 14 PLIP interactions: 7 interactions with chain F, 7 interactions with chain D Hydrophobic interactions: F:L.24, F:I.30, F:A.124, F:L.125, F:L.128, D:P.372, D:A.376, D:L.457 Hydrogen bonds: F:R.32, F:R.32, D:T.373, D:T.374 Salt bridges: D:K.453, D:K.453 SQD.5: 24 residues within 4Å: Chain D: I.293, K.296, N.359, V.417, V.424, I.428, N.431, R.432 Chain F: R.174, D.175, L.178, T.179, V.182, L.185, M.189, L.240, L.537, Y.538, R.539, T.541, V.542, V.543, V.546, D.547 21 PLIP interactions: 5 interactions with chain D, 16 interactions with chain F Hydrophobic interactions: D:V.417, D:V.417, D:V.424, F:L.178, F:L.185, F:L.240, F:L.537, F:Y.538, F:Y.538, F:Y.538, F:T.541, F:V.542, F:V.542, F:V.546, F:V.546 Hydrogen bonds: D:N.359, D:N.431 Salt bridges: F:R.174, F:R.174, F:R.174, F:R.539 SQD.7: 18 residues within 4Å: Chain F: L.300, I.303, A.304, V.306, R.366, T.424, F.425, F.428, R.432, L.436, L.499, W.506, Y.508, K.515, P.516, V.517, Q.525, L.528 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:L.300, F:I.303, F:F.425, F:F.425, F:F.428, F:F.428, F:L.499, F:L.499, F:W.506, F:W.506 Hydrogen bonds: F:A.304, F:Y.508, F:K.515, F:V.517 Salt bridges: F:R.432, F:R.432, F:R.432 SQD.12: 12 residues within 4Å: Chain A: F.85 Chain C: L.42, L.43, P.45, K.46 Chain K: L.31, V.34, Y.35, I.171, N.172, R.174 Ligands: SQD.14 16 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A, 9 interactions with chain K Hydrophobic interactions: C:L.43, C:L.43, A:F.85, A:F.85, K:L.31, K:V.34, K:Y.35, K:I.171 Hydrogen bonds: C:K.46, C:K.46, K:N.172 Salt bridges: C:K.46, K:R.174, K:R.174, K:R.174, K:R.174 SQD.14: 15 residues within 4Å: Chain A: L.74 Chain K: I.27, L.31, V.34, W.37 Chain L: P.63, I.65, N.66, R.68 Chain N: L.3, L.4, F.29, R.32, V.138 Ligands: SQD.12 11 PLIP interactions: 3 interactions with chain N, 6 interactions with chain L, 1 interactions with chain A, 1 interactions with chain K Hydrophobic interactions: N:L.4, A:L.74, K:V.34 Hydrogen bonds: N:V.138, L:P.63, L:I.65, L:N.66, L:N.66, L:R.68 Salt bridges: N:R.32, L:R.68

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

BCR.6: 12 residues within 4Å: Chain F: E.451, I.457, T.461, V.462, L.466, H.469, L.473, F.477 Chain P: P.73, M.184, F.195 Ligands: CLA.8 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain P Hydrophobic interactions: F:T.461, F:L.466, F:L.473, F:F.477, P:P.73, P:F.195

1 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.8: 3 residues within 4Å: Chain F: H.469, I.472 Ligands: BCR.6 2 PLIP interactions: 2 interactions with chain F, Hydrophobic interactions: F:I.472, F:I.472

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

SF4.9: 11 residues within 4Å: Chain I: C.73, P.74, P.78, I.98, C.103, I.104, F.105, C.106, A.107, N.108, C.109 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.73, I:C.103, I:C.106, I:C.109 SF4.10: 12 residues within 4Å: Chain I: C.63, I.64, A.65, C.66, E.67, V.68, C.69, Y.96, C.113, P.114, T.115, C.117 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.63, I:C.66, I:C.69, I:C.113 SF4.11: 12 residues within 4Å: Chain H: R.69 Chain K: A.51, C.52, C.53, G.88, T.89, G.115, A.116, C.117, M.123, C.148, P.149 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.52, K:C.53, K:C.117, K:C.148

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 2 residues within 4Å: Chain P: H.130, R.135 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schuller, J.M. et al., Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I. Nat Commun (2020)

Release Date

2020-02-19

Peptides

NAD(P)H-quinone oxidoreductase subunit 1: A
NAD(P)H-quinone oxidoreductase subunit 2: B
NAD(P)H-quinone oxidoreductase subunit 3: C
NADH dehydrogenase subunit 4: D
NAD(P)H-quinone oxidoreductase subunit 4L: E
NADH dehydrogenase subunit 5: F
NADH dehydrogenase subunit 6: G
NAD(P)H-quinone oxidoreductase subunit H: H
NAD(P)H-quinone oxidoreductase subunit I: I
NAD(P)H-quinone oxidoreductase subunit J: J
NAD(P)H-quinone oxidoreductase subunit K: 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
NAD(P)H-quinone oxidoreductase subunit O: O
Tlr0906 protein: P
Tll0220 protein: Q
Tlr0636 protein: R

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
S

Membrane

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

NAD(P)H-quinone oxidoreductase subunit 2

NAD(P)H-quinone oxidoreductase subunit 3

NADH dehydrogenase subunit 4

NAD(P)H-quinone oxidoreductase subunit 4L

NADH dehydrogenase subunit 5

NADH dehydrogenase subunit 6

NAD(P)H-quinone oxidoreductase subunit H

NAD(P)H-quinone oxidoreductase subunit I

NAD(P)H-quinone oxidoreductase subunit J

NAD(P)H-quinone oxidoreductase subunit K

NAD(P)H-quinone oxidoreductase subunit L

NAD(P)H-quinone oxidoreductase subunit M

NAD(P)H-quinone oxidoreductase subunit N

NAD(P)H-quinone oxidoreductase subunit O

Tlr0906 protein

Tll0220 protein

Tlr0636 protein

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