SMTL ID : 6nzu.1

Structure of the human frataxin-bound iron-sulfur cluster assembly complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-mer

Ligands

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

PLP.1: 11 residues within 4Å: Chain A: G.72, A.73, T.74, H.102, D.178, A.180, Q.181, S.201, H.203, K.204 Chain E: T.241 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:K.204 Hydrogen bonds: A:A.73, A:T.74, A:Q.181, A:S.201, A:K.204, E:T.241, E:T.241 Salt bridges: A:H.203 pi-Stacking: A:H.102 PLP.4: 11 residues within 4Å: Chain A: T.241 Chain E: G.72, A.73, T.74, H.102, D.178, A.180, Q.181, S.201, H.203, K.204 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:K.204 Hydrogen bonds: E:A.73, E:T.74, E:Q.181, E:S.201, A:T.241, A:T.241 Salt bridges: E:H.203 pi-Cation interactions: E:H.102

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

8Q1.2: 13 residues within 4Å: Chain A: P.17 Chain B: R.7, V.10, Y.32, R.36, A.40, F.41, N.44, K.45, V.47, I.53, D.63 Chain C: S.37 9 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:Y.32, B:R.36, B:A.40, B:K.45, B:I.53, A:P.17 Hydrogen bonds: B:N.44, C:S.37 Salt bridges: B:R.7 8Q1.5: 12 residues within 4Å: Chain E: P.17 Chain F: R.7, Y.32, A.40, F.41, N.44, K.45, V.47, I.53, L.56, D.63 Chain G: S.37 8 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: F:Y.32, F:A.40, F:K.45, F:I.53, E:P.17 Hydrogen bonds: F:N.44, G:S.37 Salt bridges: F:R.7

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain D: G.37, D.38, C.62, C.105 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.38, D:D.38, D:C.62, D:C.105 ZN.6: 4 residues within 4Å: Chain H: G.37, D.38, C.62, C.105 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.38, H:D.38, H:C.62, H:C.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fox, N.G. et al., Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism. Nat Commun (2019)

Release Date

2019-05-22

Peptides

Cysteine desulfurase, mitochondrial: AE
LYR motif-containing protein 4: BF
Acyl carrier protein: CG
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial: DH
Frataxin, mitochondrial: IJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

I
I

J
J

Cysteine desulfurase, mitochondrial

LYR motif-containing protein 4

Acyl carrier protein

Iron-sulfur cluster assembly enzyme ISCU, mitochondrial

Frataxin, mitochondrial