SMTL ID : 5wlw.1

Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.32 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

PLP.1: 13 residues within 4Å: Chain A: G.75, A.76, T.77, H.105, M.152, N.156, D.181, A.183, Q.184, S.204, H.206, K.207 Chain E: T.244 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:H.105, A:A.183, A:K.207 Hydrogen bonds: A:A.76, A:T.77, A:Q.184, A:S.204, A:K.207, E:T.244, E:T.244 Salt bridges: A:H.206 pi-Stacking: A:H.105 PLP.4: 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 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain E Hydrogen bonds: A:T.244, E:A.76, E:T.77, E:T.77, E:Q.184, E:S.204, E:S.204, E:K.207 Hydrophobic interactions: E:H.105, E:A.183, E:K.207 Salt bridges: E:H.206 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: 14 residues within 4Å: Chain B: R.6, V.9, L.10, I.36, A.39, F.40, N.43, K.44, V.46, L.55, V.65, I.66 Chain C: D.35, S.36 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.10, B:F.40, B:V.65, B:I.66 Hydrogen bonds: B:N.43, B:N.43, C:S.36 Salt bridges: B:R.6 8Q1.5: 16 residues within 4Å: Chain F: R.6, L.10, M.16, Y.31, I.36, A.39, F.40, N.43, K.44, V.46, I.52, L.55, A.59, D.62, I.66 Chain G: S.36 14 PLIP interactions: 13 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:R.6, F:L.10, F:Y.31, F:I.36, F:A.39, F:F.40, F:K.44, F:V.46, F:I.66, F:I.66 Hydrogen bonds: F:N.43, F:N.43, G:S.36 Salt bridges: F:R.6

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.330 Chain D: D.46, C.70, H.112, C.113 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:D.46, D:C.70, D:H.112, A:C.330 ZN.6: 5 residues within 4Å: Chain E: C.330 Chain H: D.46, C.70, H.112, C.113 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain E Metal complexes: H:D.46, H:D.46, H:C.70, E:C.330

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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