SMTL ID : 6ziy.1

Respiratory complex I from Thermus thermophilus, NADH dataset, major state

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: 13 residues within 4Å: Chain A: I.181, P.199, E.351, S.352, C.353, G.354, K.355, C.356, C.359, S.398, C.400, L.402, A.403 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.353, A:C.356, A:C.359, A:C.400 SF4.5: 9 residues within 4Å: Chain C: H.115, P.116, D.118, C.119, C.122, C.128, Q.131, G.233 Chain D: M.321 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.115, C:C.119, C:C.122, C:C.128 SF4.6: 10 residues within 4Å: Chain C: C.181, C.184, C.187, F.202, I.211, C.230, P.231, V.232, A.234, L.235 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.181, C:C.184, C:C.187, C:C.230 SF4.7: 10 residues within 4Å: Chain C: C.256, L.258, C.259, V.261, G.262, C.263, I.290, C.291, P.407, I.408 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.256, C:C.259, C:C.263, C:C.291 SF4.9: 10 residues within 4Å: Chain D: R.84, H.169 Chain F: C.45, C.46, G.109, A.110, C.111, G.139, C.140, P.141 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.45, F:C.46, F:C.111, F:C.140 SF4.10: 10 residues within 4Å: Chain G: H.41, C.63, A.67, I.68, I.93, C.98, I.99, F.100, C.101, C.104 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.63, G:C.98, G:C.101, G:C.104 SF4.11: 10 residues within 4Å: Chain G: C.53, I.54, G.55, C.56, S.57, L.58, C.59, V.70, Y.91, C.108 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.53, G:C.56, G:C.59, G:C.108

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain A: G.64, R.65, G.66, A.68, K.75, N.92, D.94, E.95, S.96, Y.180, G.183, E.184, I.218, N.219, N.220, P.401, L.402 Ligands: NAI.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.180, A:E.184, A:P.401, A:L.402 Hydrogen bonds: A:R.65, A:G.66, A:N.92, A:D.94, A:D.94, A:S.96, A:G.183, A:I.218, A:N.220, A:N.220 Salt bridges: A:K.75

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 18 residues within 4Å: Chain A: G.66, G.67, A.68, G.69, F.70, K.75, F.78, E.97, Y.180, E.184, E.185, K.202, F.205, P.206, S.296, T.325, P.401 Ligands: FMN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.97 Hydrogen bonds: A:F.70, A:K.75, A:E.185, A:E.185, A:K.202 Salt bridges: A:K.202, A:K.202 pi-Stacking: A:F.70, A:F.205

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

FES.4: 10 residues within 4Å: Chain B: C.83, T.85, S.87, C.88, C.124, L.125, G.126, S.127, C.128, V.133 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.83, B:C.88, B:C.124, B:C.128 FES.8: 11 residues within 4Å: Chain C: M.20, L.32, F.33, C.34, S.35, G.43, A.44, C.45, R.46, C.48, C.83 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.34, C:C.45, C:C.48, C:C.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gutierrez-Fernandez, J. et al., Key role of quinone in the mechanism of respiratory complex I. Nat Commun (2020)

Release Date

2020-09-02

Peptides

NADH-quinone oxidoreductase subunit 1: A
NADH-quinone oxidoreductase subunit 2: B
NADH-quinone oxidoreductase subunit 3: C
NADH-quinone oxidoreductase subunit 4: D
NADH-quinone oxidoreductase subunit 5: E
NADH-quinone oxidoreductase subunit 6: F
NADH-quinone oxidoreductase subunit 9: G
NADH-quinone oxidoreductase subunit 15: H
NADH-quinone oxidoreductase subunit 7: I
NADH-quinone oxidoreductase subunit 10: J
NADH-quinone oxidoreductase subunit 11: K
NADH-quinone oxidoreductase subunit 12: L
NADH-quinone oxidoreductase subunit 13: M
NADH-quinone oxidoreductase subunit 14: N
NADH-quinone oxidoreductase subunit 8: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
9

H
7

I
A

J
J

K
K

L
L

M
M

N
N

O
H

Membrane

We predict this structure to be a membrane protein.
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NADH-quinone oxidoreductase subunit 1

NADH-quinone oxidoreductase subunit 2

NADH-quinone oxidoreductase subunit 3

NADH-quinone oxidoreductase subunit 4

NADH-quinone oxidoreductase subunit 5

NADH-quinone oxidoreductase subunit 6

NADH-quinone oxidoreductase subunit 9

NADH-quinone oxidoreductase subunit 15

NADH-quinone oxidoreductase subunit 7

NADH-quinone oxidoreductase subunit 10

NADH-quinone oxidoreductase subunit 11

NADH-quinone oxidoreductase subunit 12

NADH-quinone oxidoreductase subunit 13

NADH-quinone oxidoreductase subunit 14

NADH-quinone oxidoreductase subunit 8

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