SMTL ID : 7nyu.1

Respiratory complex I from Escherichia coli - conformation 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain B: C.63, C.64, G.100, T.101, G.127, A.128, C.129, G.157, C.158, P.159 Chain C: R.250, R.270, H.355 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.63, B:C.64, B:C.129, B:C.158 SF4.4: 12 residues within 4Å: Chain E: I.179, P.197, S.350, C.351, G.352, W.353, C.354, C.357, T.396, F.397, C.398, H.400 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.351, E:C.354, E:C.357, E:C.398 SF4.6: 13 residues within 4Å: Chain F: C.151, I.152, A.153, C.154, Y.155, R.156, C.157, F.181, C.201, P.202, T.203, V.205, F.206 5 PLIP interactions: 5 interactions with chain F, pi-Cation interactions: F:F.181 Metal complexes: F:C.151, F:C.154, F:C.157, F:C.201 SF4.7: 12 residues within 4Å: Chain C: I.512 Chain F: H.99, D.102, C.103, C.106, E.108, C.112, L.114, Q.115, R.150, T.203, G.204 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:H.99, F:C.103, F:C.106, F:C.112 SF4.8: 8 residues within 4Å: Chain F: C.228, Q.230, C.231, I.233, G.234, C.235, C.263, G.266 6 PLIP interactions: 6 interactions with chain F, Metal complexes: F:C.228, F:C.228, F:C.231, F:C.235, F:C.235, F:C.263 SF4.10: 11 residues within 4Å: Chain H: C.60, V.61, A.62, C.63, N.64, L.65, C.66, C.109, T.111, A.113, I.114 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.60, H:C.63, H:C.66, H:C.109 SF4.11: 10 residues within 4Å: Chain H: I.48, C.70, V.72, C.74, C.99, I.100, F.101, C.102, G.103, C.105 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.70, H:C.99, H:C.102, H:C.105

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

FES.2: 10 residues within 4Å: Chain D: C.92, S.94, V.96, C.97, C.133, L.134, G.135, N.136, C.137, N.142 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.92, D:C.97, D:C.133, D:C.137 FES.5: 11 residues within 4Å: Chain F: F.33, C.34, W.35, G.43, A.44, C.45, R.46, Q.47, C.48, M.65, C.67 5 PLIP interactions: 5 interactions with chain F, Metal complexes: F:C.34, F:C.34, F:C.45, F:C.48, F:C.67

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 16 residues within 4Å: Chain E: G.61, R.62, G.63, K.72, N.90, E.93, Y.178, I.179, G.181, E.182, E.183, V.216, N.217, N.218, T.221, H.400 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:Y.178, E:Y.178, E:I.179, E:E.182, E:E.182, E:H.400 Hydrogen bonds: E:R.62, E:G.63, E:N.90, E:E.93, E:E.93, E:E.93, E:G.181, E:E.183, E:N.217, E:N.218, E:N.218, E:T.221 Salt bridges: E:K.72

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain F: D.617, Q.632, E.647, D.731 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.617, F:E.647, F:D.731

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolata, P. et al., Structure of Escherichia coli respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation. Elife (2021)

Release Date

2021-08-25

Peptides

NADH-quinone oxidoreductase subunit A: A
NADH-quinone oxidoreductase subunit B: B
NADH-quinone oxidoreductase subunit C/D: C
NADH-quinone oxidoreductase subunit E: D
NADH-quinone oxidoreductase subunit F: E
NADH-quinone oxidoreductase subunit G: F
NADH-quinone oxidoreductase subunit H: G
NADH-quinone oxidoreductase subunit I: H
NADH-quinone oxidoreductase subunit J: I
NADH-quinone oxidoreductase subunit K: J
NADH-quinone oxidoreductase subunit L: K
NADH-quinone oxidoreductase subunit M: L
NADH-quinone oxidoreductase subunit N: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

G
H

H
I

I
J

J
K

K
L

L
M

M
N

Membrane

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

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit C/D

NADH-quinone oxidoreductase subunit E

NADH-quinone oxidoreductase subunit F

NADH-quinone oxidoreductase subunit G

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit J

NADH-quinone oxidoreductase subunit K

NADH-quinone oxidoreductase subunit L

NADH-quinone oxidoreductase subunit M

NADH-quinone oxidoreductase subunit N

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