SMTL ID : 7d6v.1

Mycobacterium smegmatis Sdh1 in complex with UQ1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 37 residues within 4Å: Chain A: I.14, G.15, A.16, G.17, G.18, A.19, V.37, T.38, K.39, S.40, A.45, H.46, T.47, M.49, A.50, E.51, G.52, T.172, S.173, I.174, A.208, T.209, G.210, S.220, N.221, E.224, Y.225, D.228, H.388, Y.389, G.412, E.413, R.423, G.426, S.428, L.429, L.432 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:M.49 Hydrogen bonds: A:A.16, A:A.16, A:G.18, A:A.19, A:K.39, A:K.39, A:S.40, A:H.46, A:T.47, A:T.47, A:E.51, A:G.52, A:I.174, A:I.174, A:E.224, A:D.228, A:E.413, A:E.413, A:R.423, A:G.426, A:S.428, A:S.428, A:S.428, A:L.429 pi-Cation interactions: A:H.388

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

FES.2: 9 residues within 4Å: Chain B: N.53, C.54, K.55, G.57, C.59, G.60, S.61, C.62, C.74 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.54, B:C.59, B:C.62, B:C.74 FES.7: 8 residues within 4Å: Chain C: F.110, C.114, Y.115, H.155, Y.202, C.206, H.207, H.240 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.114, C:H.155, C:C.206, C:H.240

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

SF4.3: 8 residues within 4Å: Chain B: C.145, I.146, C.148, F.149, C.151, C.213, P.214, I.219 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.145, B:C.148, B:C.151, B:C.213

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.4: 12 residues within 4Å: Chain B: C.155, V.157, P.171, C.203, N.204, I.205, T.206, K.207, C.208, C.209, T.220, L.224 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.203, B:C.209

1 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.5: 6 residues within 4Å: Chain B: Y.236 Chain C: T.145, F.147, I.150, L.151, I.154 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.147, C:I.150, C:L.151, C:I.154, B:Y.236

1 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.6: 14 residues within 4Å: Chain C: L.42, F.45, R.111, L.112, Y.117, Y.121, W.126, Y.141, T.142, G.143, L.149, L.151, Q.152, L.248 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.42, C:L.42, C:F.45, C:Y.121, C:Y.121, C:W.126, C:W.126, C:L.151, C:L.248 Hydrogen bonds: C:T.142, C:G.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, X. et al., Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-04-07

Peptides

Succinate dehydrogenase subunit A: A
Fumarate reductase iron-sulfur subunit: B
Succinate dehydrogenase (Membrane anchor subunit): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Succinate dehydrogenase subunit A

Fumarate reductase iron-sulfur subunit

Succinate dehydrogenase (Membrane anchor subunit)

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