SMTL ID : 3w9t.1

pore-forming CEL-III

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-heptamer

Ligands

37 x FRU- GAL: beta-D-galactopyranose-(1-4)-beta-D-fructofuranose(Non-covalent)

FRU-GAL.1: 7 residues within 4Å: Chain A: D.23, I.24, V.25, G.26, Y.36, D.39 Ligands: CA.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.26, A:D.23, A:G.26, A:D.39 FRU-GAL.2: 5 residues within 4Å: Chain A: D.121, I.122, E.123, G.124 Ligands: CA.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.124, A:D.121, A:G.124 FRU-GAL.3: 7 residues within 4Å: Chain A: D.168, V.169, E.170, G.171, Y.181, E.184 Ligands: CA.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.170, A:G.171, A:D.168, A:G.171, A:E.184 FRU-GAL.4: 6 residues within 4Å: Chain A: D.209, V.210, E.211, G.212, Y.222 Ligands: CA.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.212, A:D.209, A:G.212, A:D.225 FRU-GAL.5: 7 residues within 4Å: Chain A: D.256, V.257, S.258, G.259, W.269, D.272 Ligands: CA.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.259, A:D.256, A:G.259, A:D.272 FRU-GAL.6: 7 residues within 4Å: Chain B: D.23, I.24, V.25, G.26, Y.36, D.39 Ligands: CA.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.26, B:I.24, B:G.26, B:D.39 FRU-GAL.7: 7 residues within 4Å: Chain B: D.121, I.122, E.123, G.124, Y.134, Q.137 Ligands: CA.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.124, B:I.122, B:G.124, B:Q.137 FRU-GAL.8: 7 residues within 4Å: Chain B: D.168, V.169, E.170, G.171, Y.181, E.184 Ligands: CA.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.171, B:D.168, B:G.171, B:E.184 FRU-GAL.9: 6 residues within 4Å: Chain B: D.209, V.210, E.211, G.212, Y.222 Ligands: CA.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.212, B:D.209, B:G.212 Water bridges: B:D.214 FRU-GAL.10: 7 residues within 4Å: Chain B: D.256, V.257, S.258, G.259, W.269, D.272 Ligands: CA.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.259, B:D.256, B:G.259 FRU-GAL.11: 7 residues within 4Å: Chain C: D.256, V.257, S.258, G.259, W.269, D.272 Ligands: CA.56 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.259, C:D.256, C:G.259, C:D.272 FRU-GAL.12: 7 residues within 4Å: Chain C: D.168, V.169, E.170, G.171, Y.181, E.184 Ligands: CA.58 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.170, C:G.171, C:D.168, C:G.171, C:E.184 FRU-GAL.13: 6 residues within 4Å: Chain C: D.209, V.210, E.211, G.212, Y.222 Ligands: CA.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.211, C:G.212, C:D.209, C:G.212 FRU-GAL.14: 7 residues within 4Å: Chain C: D.23, I.24, V.25, G.26, Y.36, D.39 Ligands: CA.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.26, C:D.23, C:G.26, C:D.39 FRU-GAL.15: 7 residues within 4Å: Chain C: D.121, I.122, E.123, G.124, Y.134, Q.137 Ligands: CA.55 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.124, C:D.121, C:G.124, C:Q.137 FRU-GAL.16: 7 residues within 4Å: Chain D: D.256, V.257, S.258, G.259, W.269, D.272 Ligands: CA.64 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.259, D:D.256, D:G.259, D:D.272 FRU-GAL.17: 8 residues within 4Å: Chain D: D.168, V.169, E.170, G.171, L.179, Y.181, E.184 Ligands: CA.63 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.171, D:D.168, D:G.171, D:E.184 FRU-GAL.18: 7 residues within 4Å: Chain D: D.23, I.24, V.25, G.26, Y.36, D.39 Ligands: CA.65 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.26, D:D.23, D:G.26, D:D.39 FRU-GAL.19: 7 residues within 4Å: Chain D: D.121, I.122, E.123, G.124, Y.134, Q.137 Ligands: CA.66 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.121, D:G.124, D:Q.137 FRU-GAL.20: 6 residues within 4Å: Chain D: D.209, V.210, E.211, G.212, Y.222 Ligands: CA.67 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.212, D:G.212, D:G.212 FRU-GAL.21: 8 residues within 4Å: Chain D: Q.1, L.3, C.4, T.5, N.6, C.49, D.51, I.84 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.1, D:T.5, D:N.6, D:N.6, D:G.50, D:D.51, D:N.6 FRU-GAL.22: 6 residues within 4Å: Chain E: D.256, V.257, S.258, G.259, W.269 Ligands: CA.71 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.259, E:D.256, E:G.259 Water bridges: E:W.269, E:D.272 FRU-GAL.23: 6 residues within 4Å: Chain E: D.209, V.210, E.211, G.212, Y.222 Ligands: CA.73 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.212, E:D.209, E:G.212, E:D.225 FRU-GAL.24: 8 residues within 4Å: Chain E: D.168, V.169, E.170, G.171, L.179, Y.181, E.184 Ligands: CA.74 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.171, E:D.168, E:G.171, E:E.184 FRU-GAL.25: 7 residues within 4Å: Chain E: D.23, I.24, V.25, G.26, Y.36, D.39 Ligands: CA.72 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.26, E:D.23, E:G.26, E:D.39 FRU-GAL.26: 9 residues within 4Å: Chain E: Q.1, L.3, C.4, T.5, N.6, C.49, G.50, D.51, I.84 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.6, E:L.3, E:T.5, E:T.5, E:N.6, E:N.6, E:D.51, E:D.51 FRU-GAL.27: 7 residues within 4Å: Chain F: D.256, V.257, S.258, G.259, W.269, D.272 Ligands: CA.80 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.259, F:D.256, F:G.259 FRU-GAL.28: 8 residues within 4Å: Chain F: D.168, V.169, E.170, G.171, L.179, Y.181, E.184 Ligands: CA.79 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.170, F:G.171, F:D.168, F:G.171, F:E.184 FRU-GAL.29: 6 residues within 4Å: Chain F: D.209, V.210, E.211, G.212, Y.222 Ligands: CA.81 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.211, F:G.212, F:D.209, F:G.212 FRU-GAL.30: 7 residues within 4Å: Chain F: D.23, I.24, V.25, G.26, Y.36, D.39 Ligands: CA.82 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.26, F:D.23, F:G.26 FRU-GAL.31: 7 residues within 4Å: Chain F: D.121, I.122, E.123, G.124, Y.134, Q.137 Ligands: CA.83 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.124, F:G.124, F:G.124, F:Y.134, F:Q.137 FRU-GAL.32: 8 residues within 4Å: Chain F: Q.1, L.3, C.4, T.5, N.6, C.49, G.50, D.51 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.6, F:L.3, F:T.5, F:T.5, F:N.6, F:G.50, F:D.51 FRU-GAL.33: 7 residues within 4Å: Chain G: D.256, V.257, S.258, G.259, W.269, D.272 Ligands: CA.88 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.259, G:D.256, G:G.259 FRU-GAL.34: 7 residues within 4Å: Chain G: D.23, I.24, V.25, G.26, Y.36, D.39 Ligands: CA.91 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.26, G:D.23, G:G.26 FRU-GAL.35: 7 residues within 4Å: Chain G: D.121, I.122, E.123, G.124, Y.134, Q.137 Ligands: CA.92 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.124, G:D.121, G:G.124, G:Q.137 FRU-GAL.36: 7 residues within 4Å: Chain G: D.209, V.210, E.211, G.212, Y.222, D.225 Ligands: CA.89 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.212, G:D.209, G:G.212, G:D.225 FRU-GAL.37: 7 residues within 4Å: Chain G: D.168, V.169, E.170, G.171, Y.181, E.184 Ligands: CA.90 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:E.170, G:G.171, G:D.168, G:G.171, G:E.184

44 x CA: CALCIUM ION(Non-covalent)

CA.38: 6 residues within 4Å: Chain A: D.23, I.24, G.26, D.39, D.43 Ligands: FRU-GAL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.23, A:I.24, A:G.26, A:D.43 CA.39: 6 residues within 4Å: Chain A: D.121, I.122, E.123, G.124, D.141 Ligands: FRU-GAL.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.121, A:I.122, A:G.124, A:D.141 CA.40: 5 residues within 4Å: Chain A: D.256, V.257, G.259, D.276 Ligands: FRU-GAL.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.256, A:V.257, A:G.259, A:D.276 CA.41: 6 residues within 4Å: Chain A: D.168, V.169, G.171, E.184, D.188 Ligands: FRU-GAL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.168, A:V.169, A:G.171, A:D.188 CA.42: 5 residues within 4Å: Chain A: D.209, V.210, G.212, D.229 Ligands: FRU-GAL.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.209, A:V.210, A:G.212, A:D.229 CA.45: 3 residues within 4Å: Chain A: D.373, K.420, I.432 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.373 CA.46: 5 residues within 4Å: Chain B: D.256, V.257, G.259, D.276 Ligands: FRU-GAL.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.256, B:V.257, B:G.259, B:D.276 CA.47: 6 residues within 4Å: Chain B: D.168, V.169, G.171, E.184, D.188 Ligands: FRU-GAL.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.168, B:V.169, B:G.171, B:D.188 CA.48: 6 residues within 4Å: Chain B: D.23, I.24, G.26, D.39, D.43 Ligands: FRU-GAL.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.23, B:I.24, B:G.26, B:D.43 CA.49: 5 residues within 4Å: Chain B: D.121, I.122, G.124, D.141 Ligands: FRU-GAL.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.121, B:I.122, B:G.124, B:D.141 CA.50: 5 residues within 4Å: Chain B: D.209, V.210, G.212, D.229 Ligands: FRU-GAL.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.209, B:V.210, B:G.212, B:D.229 CA.53: 3 residues within 4Å: Chain B: D.373, K.420, I.432 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.373 CA.54: 1 residues within 4Å: Chain B: E.123 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.123, B:E.123 CA.55: 5 residues within 4Å: Chain C: D.121, I.122, G.124, D.141 Ligands: FRU-GAL.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.121, C:I.122, C:G.124 CA.56: 5 residues within 4Å: Chain C: D.256, V.257, G.259, D.276 Ligands: FRU-GAL.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.256, C:V.257, C:G.259, C:D.276 CA.57: 6 residues within 4Å: Chain C: D.23, I.24, G.26, D.39, D.43 Ligands: FRU-GAL.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.23, C:I.24, C:G.26, C:D.43 CA.58: 6 residues within 4Å: Chain C: D.168, V.169, G.171, E.184, D.188 Ligands: FRU-GAL.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.168, C:V.169, C:G.171, C:D.188 CA.59: 5 residues within 4Å: Chain C: D.209, V.210, G.212, D.229 Ligands: FRU-GAL.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.209, C:V.210, C:G.212, C:D.229 CA.62: 2 residues within 4Å: Chain C: D.373, K.420 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.373 CA.63: 6 residues within 4Å: Chain D: D.168, V.169, G.171, E.184, D.188 Ligands: FRU-GAL.17 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.168, D:V.169, D:G.171, D:D.188 CA.64: 5 residues within 4Å: Chain D: D.256, V.257, G.259, D.276 Ligands: FRU-GAL.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.256, D:V.257, D:G.259, D:D.276 CA.65: 5 residues within 4Å: Chain D: D.23, I.24, G.26, D.43 Ligands: FRU-GAL.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.23, D:I.24, D:G.26, D:D.43 CA.66: 7 residues within 4Å: Chain D: D.121, I.122, G.124, Q.137, D.141, Q.142 Ligands: FRU-GAL.19 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.121, D:I.122, D:G.124 CA.67: 5 residues within 4Å: Chain D: D.209, V.210, G.212, D.229 Ligands: FRU-GAL.20 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.209, D:G.212, D:D.229 CA.70: 3 residues within 4Å: Chain D: D.373, K.420, I.432 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.373 CA.71: 6 residues within 4Å: Chain E: D.256, V.257, S.258, G.259, D.276 Ligands: FRU-GAL.22 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.256, E:V.257, E:G.259, E:D.276 CA.72: 6 residues within 4Å: Chain E: D.23, I.24, G.26, D.39, D.43 Ligands: FRU-GAL.25 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.23, E:I.24, E:G.26, E:D.43 CA.73: 5 residues within 4Å: Chain E: D.209, V.210, G.212, D.229 Ligands: FRU-GAL.23 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.209, E:V.210, E:G.212, E:D.229 CA.74: 5 residues within 4Å: Chain E: D.168, V.169, G.171, D.188 Ligands: FRU-GAL.24 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.168, E:V.169, E:G.171, E:D.188 CA.77: 6 residues within 4Å: Chain E: D.121, G.124, Q.137, L.139, D.141, Q.142 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.141 CA.78: 2 residues within 4Å: Chain E: D.373, I.432 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.373 CA.79: 6 residues within 4Å: Chain F: D.168, V.169, G.171, E.184, D.188 Ligands: FRU-GAL.28 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.168, F:V.169, F:G.171, F:D.188 CA.80: 5 residues within 4Å: Chain F: D.256, V.257, G.259, D.276 Ligands: FRU-GAL.27 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.256, F:V.257, F:G.259, F:D.276 CA.81: 5 residues within 4Å: Chain F: D.209, V.210, G.212, D.229 Ligands: FRU-GAL.29 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.209, F:V.210, F:G.212, F:D.229 CA.82: 6 residues within 4Å: Chain F: D.23, I.24, G.26, D.39, D.43 Ligands: FRU-GAL.30 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.23, F:I.24, F:G.26, F:D.43 CA.83: 6 residues within 4Å: Chain F: D.121, I.122, G.124, Q.137, D.141 Ligands: FRU-GAL.31 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.121, F:I.122, F:G.124 CA.86: 2 residues within 4Å: Chain F: D.373, K.420 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.373 CA.87: 1 residues within 4Å: Chain F: E.211 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.211, F:E.211 CA.88: 5 residues within 4Å: Chain G: D.256, V.257, G.259, D.276 Ligands: FRU-GAL.33 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.256, G:V.257, G:G.259, G:D.276 CA.89: 5 residues within 4Å: Chain G: D.209, V.210, G.212, D.229 Ligands: FRU-GAL.36 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.209, G:V.210, G:G.212, G:D.229 CA.90: 6 residues within 4Å: Chain G: D.168, V.169, G.171, E.184, D.188 Ligands: FRU-GAL.37 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.168, G:V.169, G:G.171, G:D.188 CA.91: 5 residues within 4Å: Chain G: D.23, I.24, G.26, D.43 Ligands: FRU-GAL.34 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.23, G:I.24, G:G.26, G:D.43 CA.92: 7 residues within 4Å: Chain G: D.121, I.122, G.124, Q.137, D.141, Q.142 Ligands: FRU-GAL.35 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.121, G:I.122, G:G.124, G:D.141 CA.95: 1 residues within 4Å: Chain G: D.373 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.373

14 x MG: MAGNESIUM ION(Non-covalent)

MG.43: 6 residues within 4Å: Chain A: N.177, V.178, N.218, V.219, D.265, V.266 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:V.178, A:V.219, A:D.265, A:V.266 MG.44: 6 residues within 4Å: Chain A: N.32, I.33, N.72, V.73, D.130, I.131 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:I.33, A:V.73, A:I.131 MG.51: 6 residues within 4Å: Chain B: N.177, V.178, N.218, V.219, D.265, V.266 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.178, B:V.219, B:D.265, B:V.266 MG.52: 6 residues within 4Å: Chain B: N.32, I.33, N.72, V.73, D.130, I.131 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.33, B:V.73, B:I.131 MG.60: 6 residues within 4Å: Chain C: N.177, V.178, N.218, V.219, D.265, V.266 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:V.178, C:V.219, C:D.265, C:V.266 MG.61: 6 residues within 4Å: Chain C: N.32, I.33, N.72, V.73, D.130, I.131 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:I.33, C:V.73, C:I.131 MG.68: 6 residues within 4Å: Chain D: N.32, I.33, N.72, V.73, D.130, I.131 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:I.33, D:V.73, D:I.131 MG.69: 6 residues within 4Å: Chain D: N.177, V.178, N.218, V.219, D.265, V.266 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:V.178, D:V.219, D:D.265, D:V.266 MG.75: 6 residues within 4Å: Chain E: N.177, V.178, N.218, V.219, D.265, V.266 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:V.178, E:V.219, E:D.265, E:V.266 MG.76: 6 residues within 4Å: Chain E: N.32, I.33, N.72, V.73, D.130, I.131 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:I.33, E:V.73, E:I.131 MG.84: 6 residues within 4Å: Chain F: N.177, V.178, N.218, V.219, D.265, V.266 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:V.178, F:V.219, F:D.265, F:V.266 MG.85: 6 residues within 4Å: Chain F: N.32, I.33, N.72, V.73, D.130, I.131 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:I.33, F:V.73, F:I.131 MG.93: 6 residues within 4Å: Chain G: N.177, V.178, N.218, V.219, D.265, V.266 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:V.178, G:V.219, G:D.265, G:V.266 MG.94: 6 residues within 4Å: Chain G: N.32, I.33, N.72, V.73, D.130, I.131 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:I.33, G:V.73, G:I.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unno, H. et al., Hemolytic lectin CEL-III heptamer reveals its transmembrane pore-formation mechanism. J.Biol.Chem. (2014)

Release Date

2014-03-19

Peptides

Hemolytic lectin CEL-III: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
G

D
B

E
F

F
E

G
D

Membrane

We predict this structure to be a membrane protein.
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Hemolytic lectin CEL-III

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