SMTL ID : 8tvt.1

Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

30 x EDO: 1,2-ETHANEDIOL

EDO.1: 5 residues within 4Å: Chain A: P.7, L.316, L.319, K.320, V.322 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: E.276, I.279, Q.280, P.295 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: K.320, H.378, R.381 Chain D: E.12 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: M.317, A.318, K.320, H.378 Chain D: V.8, Y.11, E.12 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: M.283, K.284, S.285, L.286, P.287 Ligands: P15.21 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: K.106, L.109, R.113, Y.339 Ligands: PEG.22 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: E.53, R.54, Q.57 Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: E.49, A.50, E.53 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: K.197, D.199, R.220 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: S.74, G.213, R.241, T.244, P.246 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: E.265, Y.266, K.269 Ligands: PEG.38 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: R.169, S.172, S.173, K.197 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: Q.57, D.66, P.67, R.68 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: K.161, Q.162, P.163 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: K.129, R.342, A.343, G.345 Ligand excluded by PLIP EDO.28: 1 residues within 4Å: Chain A: F.90 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain A: Q.377, K.380, R.381 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: E.263 Chain B: R.35, A.39 Ligands: PEG.38, 8Q1.45 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain A: I.219, R.220, R.221, R.224, V.225 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: G.234, G.235, Q.236 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: Y.9, V.12, P.17, F.362, T.363 Chain B: N.27 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: A.11, L.12, L.63 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain B: R.67 Ligands: PEG.40 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain B: E.42, N.43, V.46 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: K.21, R.22, F.23, R.29 Ligands: EDT.43 Ligand excluded by PLIP EDO.44: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain B: R.6 Chain C: V.29, D.35, S.36 Ligands: 8Q1.45 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain C: P.55, Y.71, H.75 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain D: G.18, S.19, R.57 Ligand excluded by PLIP EDO.52: 2 residues within 4Å: Chain D: E.75, W.76 Ligand excluded by PLIP

1 x PLP: PYRIDOXAL-5'-PHOSPHATE

PLP.3: 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 Ligands: LPH.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.184 Hydrogen bonds: A:A.76, A:T.77, A:T.77, A:N.80, A:Q.184, A:K.207 Salt bridges: A:H.206, A:K.207 pi-Stacking: A:H.105

1 x LPH: L-Propargylglycine

LPH.4: 11 residues within 4Å: Chain A: Q.13, A.14, H.105, N.156, Q.184, H.206, K.207, S.328, C.330, R.356 Ligands: PLP.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.105, A:N.156, A:Q.184, A:K.207 Salt bridges: A:R.356

3 x GOL: GLYCEROL

GOL.5: 4 residues within 4Å: Chain A: T.364, E.365, E.366 Chain B: R.34 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.270, A:E.365, B:R.34 GOL.6: 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.51: 2 residues within 4Å: Chain D: D.21, T.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.21, D:T.23, D:T.23

8 x PEG: DI(HYDROXYETHYL)ETHER

PEG.16: 5 residues within 4Å: Chain A: D.24, A.25, P.28 Chain B: R.68 Ligands: PEG.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.24 PEG.19: 4 residues within 4Å: Chain A: P.190, M.264, E.265, H.268 No protein-ligand interaction detected (PLIP) PEG.22: 5 residues within 4Å: Chain A: Q.102, R.113, Y.124 Ligands: EDO.10, PEG.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.102, A:R.113, A:R.113 PEG.24: 5 residues within 4Å: Chain A: E.116, V.122, T.123, Y.124 Ligands: PEG.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.124, A:Y.124 Water bridges: A:V.122 PEG.34: 5 residues within 4Å: Chain A: S.232, G.233, G.235, G.239, S.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.232, A:S.242 PEG.35: 5 residues within 4Å: Chain A: G.64, A.65, D.66, D.192 Ligands: DTT.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.66, A:D.192 PEG.38: 7 residues within 4Å: Chain A: Y.266 Chain B: R.35, D.38, A.39, E.42 Ligands: EDO.15, EDO.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.35, B:R.35 PEG.40: 4 residues within 4Å: Chain B: R.67, R.68 Ligands: PEG.16, EDO.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.68

2 x PG4: TETRAETHYLENE GLYCOL

PG4.17: 4 residues within 4Å: Chain A: Q.57, S.61, Q.261, Q.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.261 Water bridges: A:Q.57, A:A.65 PG4.18: 5 residues within 4Å: Chain A: R.277, N.281, V.372, E.373, 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

P15.21: 14 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, S.353, L.388 Chain D: F.61 Ligands: EDO.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.288, A:V.289, A:Y.309, A:S.353, A:S.353 Water bridges: A:A.308, A:D.347, A:D.347, A:D.347

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE

DTT.25: 11 residues within 4Å: Chain A: G.64, A.65, D.66, E.69, V.193, N.194, Y.218, R.220, R.221, R.222 Ligands: PEG.35 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.66, A:N.194, A:N.194, A:R.220

1 x PGE: TRIETHYLENE GLYCOL

PGE.30: 7 residues within 4Å: Chain A: A.25, R.54, Q.58, A.255, E.258, V.259, Q.262 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.54, A:E.258, A:Q.262, A:Q.262 Water bridges: A:R.21, A:A.25, A:R.54, A:Q.58

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

EDT.43: 9 residues within 4Å: Chain B: K.21, Y.26, R.29, T.30, V.33, K.80, I.83, E.84 Ligands: EDO.42 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.29, B:E.84 Water bridges: B:R.29 Salt bridges: B:K.21, 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

8Q1.45: 19 residues within 4Å: Chain A: R.21 Chain B: R.6, V.9, M.16, Y.31, A.39, F.40, N.43, K.44, V.46, I.52, L.55, A.59, D.62, I.66 Chain C: D.35, S.36 Ligands: EDO.31, EDO.47 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:R.6, B:V.9, B:Y.31, B:A.39, B:I.52, B:I.66 Hydrogen bonds: B:N.43, B:N.43, B:K.44, C:S.36 Salt bridges: B:R.6

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

MES.46: 7 residues within 4Å: Chain B: R.41, K.44 Chain C: Q.14, L.15, G.33, D.35, D.38 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:D.35, C:D.38, B:K.44

1 x 1PE: PENTAETHYLENE GLYCOL

1PE.50: 6 residues within 4Å: Chain D: W.76, G.79, K.80, E.84, T.87, I.88 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.80 Water bridges: D:W.76, D:K.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zangari, J. et al., D-Cysteine impairs tumor growth by inhibiting cysteine desulfurase NFS1. To Be Published

Release Date

2024-09-11

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cysteine desulfurase

LYR motif-containing protein 4

Acyl carrier protein

Iron-sulfur cluster assembly enzyme ISCU

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