SMTL ID : 8pka.1

Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (without frataxin)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 14 residues within 4Å: Chain A: G.73, A.74, T.75, N.78, H.103, C.105, M.150, N.154, D.179, A.181, Q.182, S.202, H.204, K.205 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.74, A:H.103, A:A.181, A:K.205 Hydrogen bonds: A:A.74, A:T.75, A:T.75, A:N.78, A:Q.182, A:S.202 Water bridges: A:E.76 Salt bridges: A:H.204, A:K.205 pi-Stacking: A:H.103

1 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Covalent)

8Q1.2: 15 residues within 4Å: Chain A: R.19 Chain B: R.30, V.33, R.59, I.60, A.63, F.64, N.67, K.68, V.70, L.79, D.86, I.90 Chain C: D.36, S.37 14 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:R.30, B:V.33, B:R.59, B:I.60, B:A.63, B:F.64, B:I.90, A:R.19 Hydrogen bonds: B:N.67, B:K.68, C:D.36, C:S.37, C:S.37 Salt bridges: B:R.30

1 x FE2: FE (II) ION(Non-covalent)

FE2.3: 4 residues within 4Å: Chain A: C.328 Chain D: C.37, D.39, C.63 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:D.39, D:D.39, D:C.63, A:C.328, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulz, V. et al., Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S] cluster assembly on ISCU2. Nat Commun (2024)

Release Date

2024-05-01

Peptides

Cysteine desulfurase: A
LYR motif-containing protein 4: B
Acyl carrier protein: C
Iron-sulfur cluster assembly enzyme ISCU: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cysteine desulfurase

LYR motif-containing protein 4

Acyl carrier protein

Iron-sulfur cluster assembly enzyme ISCU

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