SMTL ID : 7nz1.1

Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: S.62, C.63, C.64, G.100, T.101, A.128, C.129, Y.136, C.158, P.159 Chain B: R.250, R.270 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.63, A:C.64, A:C.129, A:C.158 SF4.3: 13 residues within 4Å: Chain D: I.179, P.197, S.350, C.351, G.352, W.353, C.354, C.357, T.396, F.397, C.398, H.400, A.401 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.351, D:C.354, D:C.357, D:C.398 SF4.6: 13 residues within 4Å: Chain E: 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 E, pi-Cation interactions: E:F.181 Metal complexes: E:C.151, E:C.154, E:C.157, E:C.201 SF4.7: 11 residues within 4Å: Chain B: I.512 Chain E: H.99, D.102, C.103, C.106, E.108, G.109, C.112, Q.115, T.203, G.204 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:H.99, E:C.103, E:C.106, E:C.112 SF4.8: 10 residues within 4Å: Chain E: C.228, Q.230, C.231, I.233, G.234, C.235, C.263, G.266, A.387, R.388 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.228, E:C.231, E:C.235, E:C.263 SF4.10: 13 residues within 4Å: Chain F: L.50, C.60, V.61, A.62, C.63, N.64, L.65, C.66, L.77, C.109, P.110, T.111, I.114 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.60, F:C.63, F:C.66, F:C.109 SF4.11: 12 residues within 4Å: Chain F: I.48, C.70, P.71, V.72, C.74, I.75, C.99, I.100, F.101, C.102, G.103, C.105 5 PLIP interactions: 5 interactions with chain F, Metal complexes: F:C.70, F:C.74, F:C.99, F:C.102, F:C.105

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

FES.2: 10 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.92, C:C.97, C:C.133, C:C.137 FES.5: 10 residues within 4Å: Chain E: Y.32, F.33, C.34, W.35, G.43, A.44, C.45, R.46, C.48, C.67 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.34, E:C.45, E:C.48, E:C.67

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 17 residues within 4Å: Chain D: G.61, R.62, G.63, K.72, N.90, D.92, E.93, M.94, Y.178, G.181, E.182, E.183, V.216, N.217, N.218, T.221, A.399 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Y.178, D:Y.178, D:E.182, D:A.399 Hydrogen bonds: D:R.62, D:G.63, D:N.90, D:E.93, D:M.94, D:G.181, D:E.183, D:N.217, D:N.218, D:N.218, D:T.221 Water bridges: D:G.66, D:G.66, D:D.92, D:D.92, D:E.95, D:G.181 Salt bridges: D:K.72

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain E: D.617, Q.632, E.647, D.731 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.617, E:E.647, E:D.731, H2O.33, H2O.41

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

2021-08-18

Peptides

NADH-quinone oxidoreductase subunit B: A
NADH-quinone oxidoreductase subunit C/D: B
NADH-quinone oxidoreductase subunit E: C
NADH-quinone oxidoreductase subunit F: D
NADH-quinone oxidoreductase subunit G: E
NADH-quinone oxidoreductase subunit I: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

D
F

E
G

F
I

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 I

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