SMTL ID : 7rtk.1

Structure of the (NIAU)2 complex with N-terminal mutation of ISCU2 Y35D at 2.5 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

PLP.1: 16 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, C.330 Chain E: T.244 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain E 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, E:T.244, E:T.244 Water bridges: A:S.74, A:E.78 Salt bridges: A:H.206, A:K.207 pi-Stacking: A:H.105 PLP.52: 16 residues within 4Å: Chain A: T.244 Chain E: 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, C.330 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:A.76, E:Q.184, E:K.207 Hydrogen bonds: E:A.76, E:T.77, E:N.80, E:Q.184, E:S.204, A:T.244 Water bridges: E:S.74, E:T.77, E:T.77, E:E.78 Salt bridges: E:H.206, E:K.207 pi-Stacking: E:H.105

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

EDO.2: 5 residues within 4Å: Chain A: E.116, V.122, T.123, Y.124 Ligands: PEG.21 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: K.320, H.378, R.381 Chain D: E.12 Ligands: EDO.6 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: M.317, A.318, K.320, H.378 Chain D: V.8, Y.11, E.12 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: M.283, K.284, S.285, L.286, P.287 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: P.7, K.320 Chain E: A.43, W.46 Ligands: GOL.3 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: K.106, L.109, R.113, Y.339 Ligands: PEG.21 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: E.49, A.50, E.53 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: S.172, K.197, D.199, R.220 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: S.74, G.213, R.241, T.244, P.246 Chain E: S.74, G.213 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: E.265, Y.266 Chain B: E.42 Ligands: PEG.38 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: Q.128, S.130, I.132, D.294 Ligand excluded by PLIP EDO.15: 9 residues within 4Å: Chain A: V.12, P.17, Y.209, G.360, R.361, F.362, T.363 Chain B: N.27 Chain E: Y.34 Ligand excluded by PLIP EDO.18: 9 residues within 4Å: Chain A: F.307, A.308, Y.309, V.310, D.349, L.350, S.353 Chain D: F.61 Ligands: P15.20 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: Q.261, Q.262 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: K.161, Q.162, P.163 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain A: F.90, S.93 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: Q.377, K.380, R.381 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain A: E.263 Chain B: R.35, A.39, N.43 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: I.219, R.220, R.221, R.224, V.225, M.240 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain A: G.234, G.235, Q.236 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain A: K.161, P.295, K.296, H.297, H.298 Ligands: PGE.24 Ligand excluded by PLIP EDO.36: 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: 4 residues within 4Å: Chain B: E.42, N.43, V.46, E.51 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain B: K.21, R.22, F.23, R.29, K.80 Ligands: EDT.43 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain B: R.6 Chain C: V.29, D.35, S.36 Ligands: 8Q1.44 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain D: V.17, G.18, S.19, K.59 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain D: T.29, L.31, D.120 Ligands: PEG.33 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain D: E.75, W.76 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain E: E.116, V.122, T.123, Y.124 Ligands: PEG.72 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain E: K.320, H.378, R.381 Chain H: E.12 Ligands: EDO.57 Ligand excluded by PLIP EDO.57: 8 residues within 4Å: Chain E: M.317, A.318, K.320, H.378 Chain H: V.8, Y.11, E.12 Ligands: EDO.56 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain E: M.283, K.284, S.285, L.286, P.287 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain A: A.43, W.46 Chain E: P.7, K.320 Ligands: GOL.54 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain E: K.106, L.109, R.113, Y.339 Ligands: PEG.72 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain E: E.49, A.50, E.53 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain E: S.172, K.197, D.199, R.220 Ligand excluded by PLIP EDO.63: 7 residues within 4Å: Chain A: S.74, G.213 Chain E: S.74, G.213, R.241, T.244, P.246 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain E: E.265, Y.266 Chain F: E.42 Ligands: PEG.89 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain E: Q.128, S.130, I.132, D.294 Ligand excluded by PLIP EDO.66: 9 residues within 4Å: Chain A: Y.34 Chain E: V.12, P.17, Y.209, G.360, R.361, F.362, T.363 Chain F: N.27 Ligand excluded by PLIP EDO.69: 9 residues within 4Å: Chain E: F.307, A.308, Y.309, V.310, D.349, L.350, S.353 Chain H: F.61 Ligands: P15.71 Ligand excluded by PLIP EDO.70: 2 residues within 4Å: Chain E: Q.261, Q.262 Ligand excluded by PLIP EDO.76: 3 residues within 4Å: Chain E: K.161, Q.162, P.163 Ligand excluded by PLIP EDO.77: 2 residues within 4Å: Chain E: F.90, S.93 Ligand excluded by PLIP EDO.78: 3 residues within 4Å: Chain E: Q.377, K.380, R.381 Ligand excluded by PLIP EDO.81: 4 residues within 4Å: Chain E: E.263 Chain F: R.35, A.39, N.43 Ligand excluded by PLIP EDO.82: 6 residues within 4Å: Chain E: I.219, R.220, R.221, R.224, V.225, M.240 Ligand excluded by PLIP EDO.83: 3 residues within 4Å: Chain E: G.234, G.235, Q.236 Ligand excluded by PLIP EDO.86: 6 residues within 4Å: Chain E: K.161, P.295, K.296, H.297, H.298 Ligands: PGE.75 Ligand excluded by PLIP EDO.87: 3 residues within 4Å: Chain F: A.11, L.12, L.63 Ligand excluded by PLIP EDO.90: 2 residues within 4Å: Chain F: R.67 Ligands: PEG.91 Ligand excluded by PLIP EDO.92: 4 residues within 4Å: Chain F: E.42, N.43, V.46, E.51 Ligand excluded by PLIP EDO.93: 6 residues within 4Å: Chain F: K.21, R.22, F.23, R.29, K.80 Ligands: EDT.94 Ligand excluded by PLIP EDO.97: 5 residues within 4Å: Chain F: R.6 Chain G: V.29, D.35, S.36 Ligands: 8Q1.95 Ligand excluded by PLIP EDO.98: 4 residues within 4Å: Chain H: V.17, G.18, S.19, K.59 Ligand excluded by PLIP EDO.100: 4 residues within 4Å: Chain H: T.29, L.31, D.120 Ligands: PEG.84 Ligand excluded by PLIP EDO.102: 2 residues within 4Å: Chain H: E.75, W.76 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: P.7, L.316, M.317, L.319, K.320, V.322 Chain E: T.41, H.42, A.43, W.46 Ligands: EDO.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:L.316, E:A.43 GOL.4: 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:E.365, A:E.366, B:R.34 GOL.50: 2 residues within 4Å: Chain D: D.21, T.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.21, D:T.23 GOL.54: 11 residues within 4Å: Chain A: T.41, H.42, A.43, W.46 Chain E: P.7, L.316, M.317, L.319, K.320, V.322 Ligands: EDO.59 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:A.43, E:L.316 GOL.55: 4 residues within 4Å: Chain E: T.364, E.365, E.366 Chain F: R.34 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:E.365, E:E.366, F:R.34 GOL.101: 2 residues within 4Å: Chain H: D.21, T.23 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:D.21, H:T.23, H:T.23

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

PG4.16: 6 residues within 4Å: Chain A: R.277, N.281, K.284, 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 PG4.67: 6 residues within 4Å: Chain E: R.277, N.281, K.284, V.372, E.373, I.376 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.281 Water bridges: E:D.369, E:E.373

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

PEG.17: 4 residues within 4Å: Chain A: P.190, M.264, E.265, H.268 Ligand excluded by PLIP PEG.21: 5 residues within 4Å: Chain A: Q.102, R.113, Y.124 Ligands: EDO.2, EDO.9 Ligand excluded by PLIP PEG.22: 5 residues within 4Å: Chain A: E.276, I.279, Q.280, P.295 Ligands: PGE.24 Ligand excluded by PLIP PEG.33: 5 residues within 4Å: Chain A: E.390, M.391, D.394, I.396 Ligands: EDO.49 Ligand excluded by PLIP PEG.34: 6 residues within 4Å: Chain A: G.64, A.65, D.66, D.192, N.194 Ligands: DTT.23 Ligand excluded by PLIP PEG.37: 7 residues within 4Å: Chain A: D.24, P.28 Chain B: R.68 Chain F: L.75, Y.76, S.77 Ligands: PEG.40 Ligand excluded by PLIP PEG.38: 6 residues within 4Å: Chain A: Y.266 Chain B: R.35, D.38, A.39, E.42 Ligands: EDO.13 Ligand excluded by PLIP PEG.40: 5 residues within 4Å: Chain B: R.67, R.68 Chain F: L.75 Ligands: PEG.37, EDO.39 Ligand excluded by PLIP PEG.68: 4 residues within 4Å: Chain E: P.190, M.264, E.265, H.268 Ligand excluded by PLIP PEG.72: 5 residues within 4Å: Chain E: Q.102, R.113, Y.124 Ligands: EDO.53, EDO.60 Ligand excluded by PLIP PEG.73: 5 residues within 4Å: Chain E: E.276, I.279, Q.280, P.295 Ligands: PGE.75 Ligand excluded by PLIP PEG.84: 5 residues within 4Å: Chain E: E.390, M.391, D.394, I.396 Ligands: EDO.100 Ligand excluded by PLIP PEG.85: 6 residues within 4Å: Chain E: G.64, A.65, D.66, D.192, N.194 Ligands: DTT.74 Ligand excluded by PLIP PEG.88: 7 residues within 4Å: Chain B: L.75, Y.76, S.77 Chain E: D.24, P.28 Chain F: R.68 Ligands: PEG.91 Ligand excluded by PLIP PEG.89: 6 residues within 4Å: Chain E: Y.266 Chain F: R.35, D.38, A.39, E.42 Ligands: EDO.64 Ligand excluded by PLIP PEG.91: 5 residues within 4Å: Chain B: L.75 Chain F: R.67, R.68 Ligands: PEG.88, EDO.90 Ligand excluded by PLIP

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

P15.20: 11 residues within 4Å: Chain A: M.283, L.286, D.288, V.289, V.290, A.308, Y.309, D.349, L.350, L.398 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.288, A:V.289 P15.71: 11 residues within 4Å: Chain E: M.283, L.286, D.288, V.289, V.290, A.308, Y.309, D.349, L.350, L.398 Ligands: EDO.69 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.288, E:D.288, E:V.289

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.23: 9 residues within 4Å: Chain A: D.66, E.69, V.193, N.194, Y.218, R.220, R.221, R.222 Ligands: PEG.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.194 DTT.74: 9 residues within 4Å: Chain E: D.66, E.69, V.193, N.194, Y.218, R.220, R.221, R.222 Ligands: PEG.85 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.194

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

PGE.24: 10 residues within 4Å: Chain A: H.268, S.272, S.275, E.276, I.279, P.295, H.298, P.300 Ligands: PEG.22, EDO.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.272, A:S.272 PGE.28: 9 residues within 4Å: Chain A: R.21, A.25, R.54, Q.58, A.255, E.258, V.259, Q.262 Chain B: D.62 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.58, A:E.258, A:Q.262 Water bridges: A:R.21, A:R.21, A:R.54 PGE.29: 2 residues within 4Å: Chain A: Y.33, R.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.54 PGE.75: 10 residues within 4Å: Chain E: H.268, S.272, S.275, E.276, I.279, P.295, H.298, P.300 Ligands: PEG.73, EDO.86 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:H.268, E:S.272, E:S.272, E:H.298 PGE.79: 9 residues within 4Å: Chain E: R.21, A.25, R.54, Q.58, A.255, E.258, V.259, Q.262 Chain F: D.62 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.58, E:Q.262 Water bridges: E:R.54, E:E.263, E:E.263 PGE.80: 2 residues within 4Å: Chain E: Y.33, R.54 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.54

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

EDT.43: 8 residues within 4Å: Chain B: K.21, Y.26, R.29, T.30, K.80, I.83, E.84 Ligands: EDO.42 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.29 Salt bridges: B:R.29, B:R.29, B:K.80 EDT.94: 8 residues within 4Å: Chain F: K.21, Y.26, R.29, T.30, K.80, I.83, E.84 Ligands: EDO.93 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.29, F:E.84 Salt bridges: F:R.29, F:R.29, F:K.80

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

8Q1.44: 18 residues within 4Å: Chain A: R.21 Chain B: R.6, V.9, M.16, Y.31, I.36, 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.46 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:R.6, B:Y.31, B:I.36, B:F.40, B:V.46, B:I.52, B:A.59 Hydrogen bonds: B:N.43, B:N.43, B:K.44, C:S.36 Salt bridges: B:R.6 8Q1.95: 18 residues within 4Å: Chain E: R.21 Chain F: R.6, V.9, M.16, Y.31, I.36, A.39, F.40, N.43, K.44, V.46, I.52, L.55, A.59, D.62 Chain G: D.35, S.36 Ligands: EDO.97 13 PLIP interactions: 2 interactions with chain G, 11 interactions with chain F Hydrogen bonds: G:S.36, G:S.36, F:N.43, F:N.43, F:K.44 Hydrophobic interactions: F:R.6, F:Y.31, F:I.36, F:F.40, F:V.46, F:I.52, F:A.59 Salt bridges: F:R.6

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

MES.45: 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 B, 1 interactions with chain C Salt bridges: B:R.41, B:K.44, C:D.38 MES.96: 7 residues within 4Å: Chain F: R.41, K.44 Chain G: Q.14, L.15, G.33, D.35, D.38 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:D.35 Salt bridges: G:D.38, F:R.41, F:K.44

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

1PE.48: 7 residues within 4Å: Chain D: W.76, K.78, 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 1PE.99: 7 residues within 4Å: Chain H: W.76, K.78, G.79, K.80, E.84, T.87, I.88 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:K.80, H:E.84

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

2021-08-25

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
A

B
B

F
B

C
C

G
C

D
D

H
D

Cysteine desulfurase, mitochondrial

LYR motif-containing protein 4

Acyl carrier protein

Iron-sulfur cluster assembly enzyme ISCU, mitochondrial

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