SMTL ID : 6wih.1

N-terminal mutation of ISCU2 (L35H36) traps Nfs1 Cys loop in the active site of ISCU2 without metal present. Structure of human mitochondrial complex Nfs1-ISCU2(L35H36)-ISD11 with E.coli ACP1 at 1.9 A resolution (NIAU)2.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

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.75, A.76, T.77, N.80, H.105, C.107, M.152, N.156, D.181, A.183, Q.184, S.204, H.206, K.207 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.76, A:Q.184, A:K.207 Hydrogen bonds: A:A.76, A:T.77, A:T.77, A:N.80, A:Q.184, A:S.204 Water bridges: A:G.75, A:E.78 Salt bridges: A:H.206, A:K.207 pi-Stacking: A:H.105

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 8 residues within 4Å: Chain A: I.219, R.220, R.221, R.224, V.225, R.226, V.227, M.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.227 Water bridges: A:V.227 PEG.16: 3 residues within 4Å: Chain A: D.24, P.28 Chain B: R.68 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.24 PEG.19: 5 residues within 4Å: Chain A: K.161, P.190, M.264, E.265, H.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.161, A:K.161 PEG.24: 3 residues within 4Å: Chain A: Q.102, Y.124 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.102 Water bridges: A:Y.124, A:Y.124 PEG.27: 5 residues within 4Å: Chain A: I.279, Q.280, M.291, P.295 Ligands: PGE.28 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.291 PEG.40: 4 residues within 4Å: Chain A: S.232, G.233, G.235, G.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.232, A:S.242 PEG.41: 5 residues within 4Å: Chain A: G.64, A.65, D.66, P.67 Ligands: PG4.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.194 PEG.47: 7 residues within 4Å: Chain A: Y.266 Chain B: R.35, D.38, A.39, E.42 Ligands: EDO.14, EDO.25 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.266 Hydrogen bonds: B:R.35, B:R.35 PEG.49: 3 residues within 4Å: Chain B: R.68 Ligands: EDO.48, EDO.50 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.68

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.7, L.316, M.317, L.319, K.320, V.322 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.316 GOL.4: 4 residues within 4Å: Chain A: K.380, R.383, E.384, W.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.380, A:E.384 Water bridges: A:K.380 GOL.5: 5 residues within 4Å: Chain A: E.139, R.169, I.170, S.173, R.174 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.139, A:S.173, A:S.173, A:R.174, A:R.174 Water bridges: A:R.169 GOL.44: 4 residues within 4Å: Chain A: R.270, T.364, E.365 Chain B: R.34 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.270, A:R.270, A:E.365, A:E.365, B:R.34 Water bridges: A:E.366 GOL.61: 2 residues within 4Å: Chain D: D.21, T.23 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.21

38 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: K.320, H.378, R.381 Chain D: E.12 Ligands: EDO.7, EDO.26 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: M.317, A.318, K.320, H.378 Chain D: V.8, Y.11, E.12 Ligands: EDO.6, EDO.26 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: M.283, K.284, S.285, L.286, P.287 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: P.7, K.320 Chain D: L.3 Ligands: GOL.3 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: K.106, L.109, E.336, Y.339 Ligands: PEG.24 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: E.49, A.50, E.53 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: S.172, K.197, D.199, R.220 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: S.74, G.213, R.241, T.244, P.246 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: E.265, Y.266 Ligands: EDO.25, PEG.47 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: Q.128, S.130, I.132, D.294, K.296 Ligand excluded by PLIP EDO.20: 10 residues within 4Å: Chain A: F.307, A.308, Y.309, D.349, L.350, S.353, L.388 Chain D: P.35, F.61 Ligands: P15.23 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: R.68, R.221 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: Q.261, Q.262 Ligands: PG4.17 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: Q.262 Chain B: R.35 Ligands: EDO.14, EDO.38, PEG.47 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: K.320, K.374, Q.377, H.378 Ligands: EDO.6, EDO.7 Ligand excluded by PLIP EDO.29: 1 residues within 4Å: Chain A: E.166 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: D.369, Y.370, E.373 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain A: Q.162, P.163 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain A: K.129, R.342, A.343, G.345 Ligand excluded by PLIP EDO.33: 1 residues within 4Å: Chain A: F.90 Ligand excluded by PLIP EDO.34: 1 residues within 4Å: Chain A: Q.377 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain A: F.90, Y.91, R.92, S.93 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain A: E.263 Chain B: R.35 Ligands: EDO.25, 8Q1.54 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain A: H.38, G.235, Q.236 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain A: K.161, P.295, K.296, H.297, H.298 Ligands: PGE.28 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain B: R.41, K.44 Chain C: G.33, D.35, D.38 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain A: Y.9, P.17, F.362, T.363 Chain B: N.27 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain B: A.11, L.12, L.63 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain B: R.67 Ligands: PEG.49, EDO.50 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain B: G.64, R.67, R.68 Ligands: EDO.48, PEG.49 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain B: E.42, N.43, V.46, E.51 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain B: K.21, R.22, F.23, R.29, K.80 Ligands: EDT.53 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain B: R.6 Chain C: V.29, A.34, D.35, S.36 Ligands: 8Q1.54 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain B: R.37 Chain C: Q.14, L.15, D.38, E.41, L.42 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain C: P.55, E.58, Y.71, H.75 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain D: G.18, S.19, R.57 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain D: T.29, L.31, D.120 Ligand excluded by PLIP EDO.62: 2 residues within 4Å: Chain D: E.75, W.76 Ligand excluded by PLIP

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.17: 9 residues within 4Å: Chain A: Q.57, A.60, S.61, G.64, A.65, Q.261, Q.262 Ligands: EDO.22, PEG.41 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.65, A:Q.261, A:Q.262 Water bridges: A:Q.57, A:S.61, A:G.64 PG4.18: 5 residues within 4Å: Chain A: R.277, N.281, K.284, V.372, I.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.281 Water bridges: A:D.369, A:E.373

1 x P15: 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL(Non-covalent)

P15.23: 13 residues within 4Å: Chain A: M.283, L.286, P.287, D.288, V.289, V.290, A.308, Y.309, D.349, L.350, L.398 Chain D: P.35 Ligands: EDO.20 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:V.289, A:D.349 Water bridges: A:D.288, A:D.288, A:W.403, D:A.36

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.28: 10 residues within 4Å: Chain A: H.268, S.272, S.275, E.276, I.279, P.295, H.298, P.300 Ligands: PEG.27, EDO.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.272, A:S.272 PGE.36: 8 residues within 4Å: Chain A: R.21, A.25, R.54, Q.58, A.255, E.258, V.259, Q.262 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.54, A:Q.58, A:E.258, A:Q.262 Water bridges: A:R.21 PGE.37: 1 residues within 4Å: Chain A: R.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.54 Water bridges: A:Y.29, A:Y.33

1 x EDT: {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID(Non-covalent)

EDT.53: 10 residues within 4Å: Chain A: E.366 Chain B: K.21, Y.26, R.29, T.30, V.33, K.80, I.83, E.84 Ligands: EDO.52 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:E.366, B:R.29, B:E.84 Water bridges: B:R.29 Salt bridges: B:R.29, B:R.29, B:K.80, B:E.84

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

8Q1.54: 17 residues within 4Å: Chain B: R.6, V.9, M.16, R.35, A.39, F.40, N.43, K.44, V.46, I.52, L.55, A.59, D.62 Chain C: D.35, S.36 Ligands: EDO.38, EDO.55 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.9, B:R.35, B:F.40, B:I.52 Hydrogen bonds: B:N.43, B:N.43, B:K.44, C:S.36 Salt bridges: B:R.6

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.59: 6 residues within 4Å: Chain D: W.76, G.79, K.80, E.84, T.87, I.88 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.80, D:T.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freibert, S.A. et al., The essential function of ISCU2 and its conserved N-terminus in Fe/S cluster biogenesis. To Be Published

Release Date

2020-05-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cysteine desulfurase, mitochondrial

LYR motif-containing protein 4

Acyl carrier protein

Iron-sulfur cluster assembly enzyme ISCU, mitochondrial

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