SMTL ID : 7awt.1

E. coli NADH quinone oxidoreductase hydrophilic arm

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: S.62, C.63, C.64, G.100, T.101, A.128, C.129, M.135, G.157, C.158, P.159 Chain B: R.270, H.355 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.63, A:C.64, A:C.129, A:C.158 SF4.4: 11 residues within 4Å: Chain D: I.179, P.197, C.351, C.354, C.357, R.358, 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 SF4.8: 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 SF4.9: 10 residues within 4Å: Chain B: I.512 Chain E: H.99, D.102, C.103, C.106, E.108, C.112, Q.115, T.203, G.204 6 PLIP interactions: 6 interactions with chain E, Salt bridges: E:D.102, E:E.108 Metal complexes: E:H.99, E:C.103, E:C.106, E:C.112 SF4.10: 10 residues within 4Å: Chain E: C.228, Q.230, C.231, I.233, C.235, L.262, C.263, R.265, G.266, R.388 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.228, E:C.231, E:C.235, E:C.263 SF4.17: 13 residues within 4Å: Chain F: C.60, V.61, A.62, C.63, N.64, L.65, C.66, L.77, C.109, P.110, T.111, A.113, I.114 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.60, F:C.63, F:C.66, F:C.109 SF4.18: 10 residues within 4Å: Chain F: I.48, C.70, V.72, C.74, 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: 9 residues within 4Å: Chain C: C.92, S.94, V.96, C.97, C.133, L.134, 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.7: 9 residues within 4Å: Chain E: Y.32, C.34, W.35, V.42, G.43, 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

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain C: E.70 Chain E: Y.173 Chain F: V.175 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain D: K.72, A.205, T.214, C.215 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain E: D.617, Q.632, E.647, D.729, D.731 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.617, E:E.647, E:D.731 MG.12: 1 residues within 4Å: Chain E: N.137 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain E: D.17, D.412 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain E: H.653 No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain E: E.108, V.198, C.201, T.203, F.206 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:V.198, E:T.203, E:F.206

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 19 residues within 4Å: Chain D: G.61, R.62, G.63, A.65, 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, H.400 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:Y.178, D:Y.178, D:E.182, D:A.399, D:H.400 Hydrogen bonds: D:G.63, D:G.64, D:N.90, D:D.92, D:M.94, D:G.181, D:E.183, D:N.217, D:N.218, D:T.221 Water bridges: D:E.183 Salt bridges: D:K.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schimpf, J. et al., Structure of the peripheral arm of a minimalistic respiratory complex I. Structure (2022)

Release Date

2021-09-15

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: 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

NADH-quinone oxidoreductase subunit I

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