SMTL ID : 9ojn.1

Structure of Mycobacterium smegmatis EtfD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

monomer

Ligands

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 12 residues within 4Å: Chain A: L.31, T.32, I.35, R.36, K.40, G.46, L.235, L.240, G.243, L.244, F.251, W.292 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.31, A:L.31, A:L.244 Hydrogen bonds: A:G.46 Salt bridges: A:R.36

1 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.2: 10 residues within 4Å: Chain A: T.81, F.85, Y.92, V.126, I.166, M.227, F.230, V.234, H.239 Ligands: HEM.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.126, A:I.166, A:F.230, A:F.230, A:V.234 pi-Stacking: A:F.85

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 23 residues within 4Å: Chain A: V.62, L.68, P.74, H.78, T.81, M.82, F.85, F.86, F.133, R.137, R.150, L.163, I.166, H.239, H.241, I.242, A.245, T.302, C.304, R.306, P.423, V.424 Ligands: MQ9.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:V.62, A:L.68, A:F.85, A:F.85, A:F.86, A:F.133, A:I.166, A:I.242, A:A.245, A:T.302, A:P.423, A:V.424 Salt bridges: A:R.137, A:R.150, A:R.306 Metal complexes: A:H.78, A:H.241

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

SF4.4: 12 residues within 4Å: Chain A: C.301, T.302, E.303, C.304, G.305, C.307, K.323, C.422, P.423, V.424, I.426, H.428 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.301, A:C.304, A:C.307, A:C.422 SF4.5: 12 residues within 4Å: Chain A: C.311, P.312, L.320, C.412, T.413, N.414, C.415, G.416, A.417, C.418, I.429, I.432 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.311, A:C.412, A:C.415, A:C.418

1 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)

9S8.6: 13 residues within 4Å: Chain A: P.582, H.583, H.634, P.636, C.637, F.638, C.672, C.673, A.675, G.676, C.709, F.711, C.712 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:H.583, A:C.637, A:C.672, A:C.673, A:C.709

1 x 01: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane

01.7: 10 residues within 4Å: Chain A: P.463, G.502, C.503, A.504, C.538, T.539, C.581, H.583, C.584, F.711 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.503, A:C.538, A:C.581, A:C.584

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Courbon, G.M. et al., Mycobacterial EtfD contains an unusual linear [3Fe-4S] cluster and enables beta oxidation to drive proton pumping by the electron transport chain. To Be Published

Release Date

2025-05-21

Peptides

Iron-sulfur-binding reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Iron-sulfur-binding reductase