SMTL ID : 8e9g.1

Mycobacterial respiratory complex I with both quinone positions modelled

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-mer

Ligands

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

SF4.1: 14 residues within 4Å: Chain B: A.36, C.37, C.38, G.74, R.75, G.101, V.102, C.103, F.110, G.131, C.132, P.133 Chain E: R.99, N.186 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.37, B:C.38, B:C.103, B:C.132 SF4.6: 11 residues within 4Å: Chain G: H.110, P.111, D.113, C.114, C.117, G.120, C.123, L.125, Q.126, V.215, G.216 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain G, pi-Cation interactions: E:F.361 Metal complexes: G:H.110, G:C.114, G:C.117, G:C.123 SF4.7: 13 residues within 4Å: Chain G: C.163, V.164, L.165, C.166, A.167, R.168, C.169, V.193, C.213, P.214, V.215, A.217, L.218 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.163, G:C.166, G:C.169, G:C.213 SF4.8: 12 residues within 4Å: Chain G: C.239, H.241, C.242, S.244, G.245, C.246, N.273, C.274, K.276, G.277, P.402, I.403 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.239, G:C.242, G:C.246, G:C.274 SF4.10: 14 residues within 4Å: Chain H: I.180, P.198, S.350, C.351, G.352, K.353, C.354, C.357, R.358, S.395, F.396, C.397, L.399, G.400 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.351, H:C.354, H:C.357, H:C.397 SF4.12: 11 residues within 4Å: Chain I: H.42, C.64, I.69, C.99, I.100, G.101, C.102, G.103, L.104, C.105, M.116 5 PLIP interactions: 5 interactions with chain I, Metal complexes: I:H.42, I:C.64, I:C.99, I:C.102, I:C.105 SF4.13: 14 residues within 4Å: Chain I: L.44, C.54, I.55, G.56, C.57, E.58, L.59, C.60, V.71, Y.92, C.109, T.111, A.113, L.114 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.54, I:C.57, I:C.60, I:C.109

2 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.2: 34 residues within 4Å: Chain B: W.29, F.33, G.34, L.35, A.39, I.40, M.42, M.43, E.58, R.59, F.60 Chain C: F.17, S.21 Chain E: P.50, H.53, Y.102, T.152, M.155, M.160, F.164 Chain J: L.29, V.32, L.33, I.36, R.40, L.64, D.66, G.67, L.70, L.244, A.247, M.250, L.251 Ligands: MQ9.14 23 PLIP interactions: 12 interactions with chain J, 8 interactions with chain B, 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: J:L.29, J:V.32, J:L.33, J:I.36, J:R.40, J:L.64, J:D.66, J:L.70, J:L.244, J:M.250, J:L.251, J:L.251, B:W.29, B:A.39, B:I.40, B:E.58, B:R.59, B:F.60, B:F.60, B:F.60, E:F.164, C:F.17 pi-Stacking: E:H.53 MQ9.14: 25 residues within 4Å: Chain B: W.29, E.58, R.59 Chain C: F.17, S.21 Chain J: V.26, L.29, L.30, V.32, L.33, I.36, R.40, L.64, G.67, I.68, L.70, A.71, L.244, F.246, A.247, M.250, L.251, Y.254, R.309 Ligands: MQ9.2 24 PLIP interactions: 21 interactions with chain J, 3 interactions with chain B Hydrophobic interactions: J:V.26, J:L.29, J:L.29, J:L.29, J:L.30, J:L.33, J:I.36, J:I.36, J:L.64, J:I.68, J:L.70, J:A.71, J:L.244, J:L.244, J:A.247, J:M.250, J:L.251, J:L.251, J:Y.254, B:W.29, B:E.58, B:R.59 Hydrogen bonds: J:R.309, J:R.309

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

FES.3: 10 residues within 4Å: Chain F: C.107, N.109, L.111, C.112, C.148, N.149, A.150, A.151, C.152, V.157 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.107, F:C.112, F:C.148, F:C.152 FES.4: 11 residues within 4Å: Chain G: R.46, F.47, C.48, D.49, G.57, C.59, R.60, Q.61, C.62, A.74, C.76 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.48, G:C.59, G:C.62, G:C.76

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 19 residues within 4Å: Chain G: R.331, Y.340, R.497, R.498, G.564, G.565, V.566, E.567, D.570, L.590, L.592, R.593, V.607, K.613, D.638, R.700, G.706, R.707, L.708 20 PLIP interactions: 20 interactions with chain G Hydrogen bonds: G:Y.340, G:E.567, G:D.570, G:D.570, G:L.590, G:L.592, G:R.593, G:R.707, G:R.707, G:R.707, G:L.708 Salt bridges: G:K.276, G:R.331, G:R.331, G:R.497, G:R.498, G:R.498, G:D.638, G:R.700, G:R.700

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 6 residues within 4Å: Chain H: C.334, V.336, R.337, E.372, H.421, C.426 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.334, H:E.372, H:H.421, H:C.426

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.11: 20 residues within 4Å: Chain H: G.54, R.55, G.56, A.58, K.65, N.91, D.93, E.94, S.95, Y.179, I.180, G.182, E.183, E.184, V.217, N.218, N.219, S.222, A.398, L.399 20 PLIP interactions: 20 interactions with chain H Hydrophobic interactions: H:Y.179, H:Y.179, H:I.180, H:E.183, H:E.183, H:A.398, H:L.399 Hydrogen bonds: H:R.55, H:G.56, H:N.91, H:D.93, H:S.95, H:G.182, H:E.184, H:V.217, H:N.218, H:N.219, H:N.219, H:S.222 Salt bridges: H:K.65

1 x XP2: (2R)-3-{[(R)-hydroxy({(1S,2R,3R,4R,5S,6S)-3,4,5-trihydroxy-2-(alpha-D-mannopyranosyloxy)-6-[(6-O-undecanoyl-beta-D-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate(Non-covalent)

XP2.15: 19 residues within 4Å: Chain M: P.166, S.167, T.170, K.173, K.174, V.177, V.178, P.236, D.553, N.556, F.560, M.561, G.564, Q.565, T.568 Chain O: I.315, L.440, W.447, Q.450 20 PLIP interactions: 17 interactions with chain M, 3 interactions with chain O Hydrophobic interactions: M:V.177, M:P.236, M:N.556, M:F.560, M:F.560, M:F.560, M:F.560, M:F.560, M:M.561, M:Q.565, O:I.315, O:L.440 Hydrogen bonds: M:T.170, M:D.553, M:Q.565, O:Q.450 Salt bridges: M:K.173, M:K.173, M:K.173, M:K.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, Y. et al., Structure of mycobacterial respiratory complex I. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2022-10-12

Peptides

Two-component system response regulator: A
NADH-quinone oxidoreductase subunit B: B
NADH-quinone oxidoreductase subunit A: C
NADH-quinone oxidoreductase subunit C: D
NADH-quinone oxidoreductase subunit D: E
NADH-quinone oxidoreductase subunit E: F
NADH-quinone oxidoreductase subunit G: G
NADH-quinone oxidoreductase subunit F: H
NADH-quinone oxidoreductase subunit I: I
NADH-quinone oxidoreductase subunit H: J
NADH-quinone oxidoreductase subunit J: K
NADH-quinone oxidoreductase subunit K: L
NADH-quinone oxidoreductase, L subunit: M
NADH-quinone oxidoreductase subunit N: N
NADH-quinone oxidoreductase, M subunit: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
B

C
A

D
C

E
D

F
E

G
G

H
F

I
I

J
H

K
J

L
K

M
L

N
N

O
M

Membrane

We predict this structure to be a membrane protein.
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Two-component system response regulator

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit A

NADH-quinone oxidoreductase subunit C

NADH-quinone oxidoreductase subunit D

NADH-quinone oxidoreductase subunit E

NADH-quinone oxidoreductase subunit G

NADH-quinone oxidoreductase subunit F

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit J

NADH-quinone oxidoreductase subunit K

NADH-quinone oxidoreductase, L subunit

NADH-quinone oxidoreductase subunit N

NADH-quinone oxidoreductase, M subunit

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