SMTL ID : 5wkp.1

Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and Iron-Sulfur Cluster Scaffold Protein ISCU1, and E. coli ACP1 protein at 3.15A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: G.75, A.76, T.77, H.105, C.107, M.152, N.156, D.181, A.183, Q.184, S.204, H.206, K.207 Chain E: T.244 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:A.76, A:H.105, A:A.183, A:K.207 Hydrogen bonds: A:A.76, A:T.77, A:Q.184, A:S.204, E:T.244, E:T.244, E:T.244 Salt bridges: A:H.206 pi-Stacking: A:H.105 PLP.3: 14 residues within 4Å: Chain A: T.244 Chain E: G.75, A.76, T.77, H.105, C.107, M.152, N.156, D.181, A.183, Q.184, S.204, H.206, K.207 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:H.105, E:A.183, E:K.207 Hydrogen bonds: E:A.76, E:T.77, E:Q.184, E:S.204, A:T.244, A:T.244 Salt bridges: E:H.206, E:K.207 pi-Stacking: E:H.105

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

8Q1.2: 12 residues within 4Å: Chain B: V.9, M.16, A.39, F.40, N.43, K.44, V.46, I.52, L.55, D.62 Chain C: D.35, S.36 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.39, B:K.44, B:V.46, B:I.52 Hydrogen bonds: B:N.43, C:S.36 8Q1.4: 16 residues within 4Å: Chain F: R.6, V.9, L.10, M.16, A.32, A.39, F.40, N.43, K.44, V.46, I.52, L.55, A.59, D.62 Chain G: D.35, S.36 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:V.9, F:L.10, F:A.32, F:A.39, F:K.44, F:I.52 Hydrogen bonds: F:N.43, F:N.43, G:S.36 Salt bridges: F:R.6, F:K.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boniecki, M.T. et al., Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Nat Commun (2017)

Release Date

2017-11-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Cysteine desulfurase, mitochondrial

LYR motif-containing protein 4

Acyl carrier protein

Iron-sulfur cluster assembly enzyme ISCU, mitochondrial

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