SMTL ID : 6wi2.1

Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.76, A:A.183, 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:S.74, A:E.78 Salt bridges: A:H.206, A:K.207 pi-Stacking: A:H.105

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

EDO.2: 4 residues within 4Å: Chain A: R.270, T.364, E.365 Chain B: R.34 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: E.116, V.122, T.123, Y.124 Ligands: PEG.27 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: Y.29, L.30, Y.34, P.248 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: M.317, A.318, K.320, H.378 Chain D: V.8, Y.11, E.12 Ligands: PEG.39 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: M.283, K.284, S.285, L.286, P.287 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: P.7, K.320 Chain D: L.3 Ligands: GOL.8 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: K.106, L.109, R.113, Y.339 Ligands: PEG.27 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: E.53, R.54, Q.57 Ligands: EDO.14 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: E.49, A.50, E.53 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: K.197, D.199, R.220 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: S.74, G.213, R.241, T.244, P.246 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: E.265, Y.266 Chain B: E.42 Ligands: EDO.45 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: Q.128, S.130, I.132, D.294 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: R.169, S.172, S.173, K.197 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: R.68, R.221 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain A: Q.261 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: Q.57, D.66, P.67, R.68 Ligands: PEG.6 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: E.365, E.366, D.369 Ligand excluded by PLIP EDO.31: 1 residues within 4Å: Chain A: E.166 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain A: D.369, Y.370, E.373 Ligand excluded by PLIP EDO.33: 1 residues within 4Å: Chain A: F.90 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: Q.377, K.380, R.381 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain A: E.263 Chain B: R.35 Ligands: 8Q1.50 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain A: K.161, P.295, K.296, H.297, H.298 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain A: Y.9, P.17, F.362, T.363 Chain B: N.27 Ligand excluded by PLIP EDO.42: 2 residues within 4Å: Chain B: L.12, A.15 Ligand excluded by PLIP EDO.43: 2 residues within 4Å: Chain B: K.60, R.61 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain A: Y.266 Chain B: D.38 Ligands: EDO.17 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Chain B: R.67 Ligands: PEG.47 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain B: K.21, R.22, F.23, R.29, K.80 Ligands: EDT.49 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain B: R.6 Chain C: V.29, D.35, S.36 Ligands: 8Q1.50 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain C: P.55, Y.71, H.75 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain D: Q.6, K.95, E.96, C.98 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain A: E.384 Chain D: G.18, K.59 Ligands: EDO.55 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain D: G.18, S.19, R.57 Ligands: EDO.54 Ligand excluded by PLIP EDO.58: 2 residues within 4Å: Chain D: E.75, W.76 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: K.380, R.383, E.384, W.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.380, A:E.384 GOL.8: 7 residues within 4Å: Chain A: P.7, L.316, M.317, L.319, K.320, V.322 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.316 GOL.57: 2 residues within 4Å: Chain D: D.21, T.23 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.21

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

PEG.5: 8 residues within 4Å: Chain A: I.219, R.220, R.221, R.224, V.225, R.226, V.227, M.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.224, A:V.227, A:V.227 PEG.6: 6 residues within 4Å: Chain A: G.64, A.65, D.66, N.194 Ligands: PG4.20, EDO.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.194 Water bridges: A:G.64 PEG.19: 3 residues within 4Å: Chain A: D.24, P.28 Chain B: R.68 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.24, A:A.25 PEG.22: 4 residues within 4Å: Chain A: P.190, M.264, E.265, H.268 No protein-ligand interaction detected (PLIP) PEG.27: 5 residues within 4Å: Chain A: Q.102, R.113, Y.124 Ligands: EDO.3, EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.102, A:R.113, A:R.113 PEG.29: 4 residues within 4Å: Chain A: I.279, Q.280, M.291, P.295 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.291 PEG.37: 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.39: 7 residues within 4Å: Chain A: K.320, K.374, Q.377, H.378, R.381 Chain D: E.12 Ligands: EDO.9 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.374, A:R.381, A:R.381 Water bridges: A:R.381, D:E.12 PEG.40: 1 residues within 4Å: Chain A: Y.33 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.29, A:Y.33, A:Y.33 PEG.47: 3 residues within 4Å: Chain B: R.67, R.68 Ligands: EDO.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.68

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

PG4.20: 8 residues within 4Å: Chain A: Q.57, A.60, S.61, G.64, A.65, Q.261, Q.262 Ligands: PEG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.261, A:Q.262 Water bridges: A:G.64 PG4.21: 4 residues within 4Å: Chain A: R.277, N.281, 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 ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.26: 10 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.288, A:V.289, A:D.349 Water bridges: A:Y.309

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

PGE.35: 8 residues within 4Å: Chain A: R.21, A.25, R.54, Q.58, A.255, E.258, V.259, Q.262 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.54, A:E.258, A:Q.262 Water bridges: A:R.21, A:R.21, A:A.25, A:R.54, A:R.54, A:R.54, A:Q.58

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.44: 8 residues within 4Å: Chain B: R.37, R.41, K.44 Chain C: Q.14, L.15, G.33, D.35, D.38 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:D.38, B:R.41, B:K.44

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

EDT.49: 9 residues within 4Å: Chain A: E.366 Chain B: K.21, Y.26, R.29, T.30, V.33, I.83, E.84 Ligands: EDO.48 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Salt bridges: C:E.48, A:E.366, B:R.29 Hydrogen bonds: A:E.366, B:R.29

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

8Q1.50: 17 residues within 4Å: Chain A: R.21 Chain B: R.6, V.9, M.16, 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.36, EDO.51 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.9, B:A.39, 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.56: 7 residues within 4Å: Chain D: W.76, K.78, G.79, K.80, E.84, T.87, I.88 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.80

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

2020-04-22

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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