SMTL ID : 8qc1.1

Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

8 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.1: 6 residues within 4Å: Chain A: F.164, K.165, L.168, Y.169, L.172 Chain B: I.656 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.164, A:F.164, A:K.165, A:L.168, A:L.168, A:Y.169, A:L.172, B:I.656 3PH.2: 8 residues within 4Å: Chain A: P.380, A.381, A.384, R.462, I.469, A.470 Chain B: R.21 Ligands: 3PE.14 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.384, A:I.469, A:A.470 Hydrogen bonds: A:R.462, A:R.462 Salt bridges: A:R.462, B:R.21, B:R.21, B:R.21 3PH.3: 8 residues within 4Å: Chain A: W.36, L.39, L.101, W.104, Q.105, T.458, R.460, W.463 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.36, A:W.36, A:L.39, A:L.101, A:L.101, A:W.104, A:W.463, A:W.463 Hydrogen bonds: A:Q.105, A:T.458 Salt bridges: A:R.460 3PH.5: 4 residues within 4Å: Chain A: L.21, F.22, R.24 Ligands: 3PE.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.21 Salt bridges: A:R.24 3PH.9: 11 residues within 4Å: Chain A: L.53, F.54, L.87, L.90, L.91, F.94, F.348, M.471, L.475, L.481, V.482 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.53, A:L.87, A:L.90, A:F.94, A:F.94, A:F.348, A:L.475, A:L.481, A:V.482 3PH.10: 8 residues within 4Å: Chain A: F.10, H.69, A.70, W.71, Y.77, L.135, L.138, F.139 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.10, A:F.10, A:W.71, A:Y.77, A:L.135, A:L.138, A:F.139 Hydrogen bonds: A:A.70 Salt bridges: A:H.69, A:H.69 3PH.12: 13 residues within 4Å: Chain A: L.304, W.436, R.439 Chain B: A.167, M.170, K.171, I.174, L.243, L.244, Y.628, F.632, V.633, K.637 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.174, B:L.243, B:L.244, B:F.632, B:F.632, B:F.632, B:F.632, B:F.632, B:V.633, A:L.304, A:W.436 Salt bridges: B:K.637, A:R.439 3PH.15: 8 residues within 4Å: Chain B: F.216, R.219, W.221, N.222, N.225, L.226, F.229, D.287 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.216, B:W.221, B:W.221, B:L.226, B:F.229, B:F.229, B:F.229 Hydrogen bonds: B:N.222, B:N.225, B:D.287 Salt bridges: B:R.219

4 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.4: 11 residues within 4Å: Chain A: I.17, A.20, L.21, R.24, K.111, E.112, I.115, A.116, I.145, L.149 Ligands: 3PH.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.17, A:I.17, A:A.20, A:E.112, A:I.115, A:I.145, A:L.149 Hydrogen bonds: A:K.111, A:K.111 Salt bridges: A:R.24, A:K.111 3PE.6: 11 residues within 4Å: Chain A: L.176, V.179, A.183, L.208, M.217, L.220, L.221, L.223, A.224, A.227 Ligands: 3PE.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.176, A:V.179, A:L.208, A:L.223, A:A.227 3PE.7: 12 residues within 4Å: Chain A: L.208, L.209, T.212, V.213, V.214, M.219, L.223, F.226, V.283, A.284, Y.287 Ligands: 3PE.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.208, A:L.209, A:L.223, A:L.223, A:F.226, A:A.284, A:Y.287, A:Y.287 Hydrogen bonds: A:V.214, A:Y.287 3PE.14: 18 residues within 4Å: Chain A: V.376, P.380, A.383, A.384, M.387, F.388, M.391, Y.438, L.473 Chain B: G.17, W.20, R.21, H.113, R.117, Y.121, F.124, Y.160 Ligands: 3PH.2 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.124, B:F.124, A:A.384, A:L.473 Hydrogen bonds: B:R.21, B:H.113, B:H.113 Water bridges: B:R.117, B:R.117, B:R.117 Salt bridges: B:R.117, B:R.117

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 5 residues within 4Å: Chain A: P.286, Y.287, W.290, L.291, W.418 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.287, A:W.290, A:W.290, A:W.290, A:W.290, A:W.290, A:L.291, A:W.418, A:W.418

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 2 residues within 4Å: Chain A: L.197, P.275 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.197, A:P.275, H2O.2, H2O.2

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.13: 18 residues within 4Å: Chain B: F.301, T.305, L.308, V.309, C.436, F.437, F.440, R.444, T.592, F.596, Y.597, P.604, R.605, L.607, A.608, L.614, Y.615, W.622 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.301, B:T.305, B:F.437, B:F.440, B:F.440, B:T.592, B:F.596, B:L.607, B:L.614, B:W.622, B:W.622 Salt bridges: B:R.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ivanov, B.S. et al., Structure of the turnover-ready state of an ancestral respiratory complex I. Nat Commun (2024)

Release Date

2024-09-11

Peptides

NADH dehydrogenase subunit M: A
NADH dehydrogenase subunit L: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
L

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase subunit M

NADH dehydrogenase subunit L

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