SMTL ID : 4nre.2 (1 other biounit)

The structure of human 15-lipoxygenase-2 with a substrate mimic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

homo-hexamer

Ligands

6 x FE2: FE (II) ION(Non-covalent)

FE2.1: 7 residues within 4Å: Chain A: H.393, H.398, H.573, S.577, V.694, I.696 Ligands: C8E.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.393, A:H.398, A:H.573, H2O.1, H2O.1 FE2.21: 7 residues within 4Å: Chain B: H.393, H.398, H.573, S.577, V.694, I.696 Ligands: C8E.22 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.393, B:H.398, B:H.573, H2O.15, H2O.15 FE2.41: 7 residues within 4Å: Chain C: H.393, H.398, H.573, S.577, V.694, I.696 Ligands: C8E.42 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.393, C:H.398, C:H.573, H2O.29, H2O.29 FE2.61: 7 residues within 4Å: Chain D: H.393, H.398, H.573, S.577, V.694, I.696 Ligands: C8E.62 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.393, D:H.398, D:H.573, H2O.43, H2O.43 FE2.81: 7 residues within 4Å: Chain E: H.393, H.398, H.573, S.577, V.694, I.696 Ligands: C8E.82 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.393, E:H.398, E:H.573, H2O.57, H2O.57 FE2.101: 7 residues within 4Å: Chain F: H.393, H.398, H.573, S.577, V.694, I.696 Ligands: C8E.102 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.393, F:H.398, F:H.573, H2O.71, H2O.71

12 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.2: 28 residues within 4Å: Chain A: F.204, F.385, E.389, H.393, L.394, H.398, I.432, N.433, L.435, A.436, L.439, L.440, V.446, V.447, R.449, T.451, F.458, D.622, V.623, L.625, A.626, L.627, L.629, L.630, I.696 Chain C: P.97, L.98 Ligands: FE2.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.440, A:L.625, A:A.626, A:L.629, A:L.630, C:P.97, C:L.98 Water bridges: A:H.398, A:H.398 C8E.3: 9 residues within 4Å: Chain A: S.210, A.213, E.214 Chain D: K.216, I.217, G.219, D.222 Chain F: L.61 Ligands: C8E.63 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.217 C8E.22: 28 residues within 4Å: Chain A: P.97, L.98 Chain B: F.204, F.385, E.389, H.393, L.394, H.398, I.432, N.433, L.435, A.436, L.439, L.440, V.446, V.447, R.449, T.451, F.458, D.622, V.623, L.625, A.626, L.627, L.629, L.630, I.696 Ligands: FE2.21 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.440, B:L.625, B:A.626, B:L.629, B:L.630, A:P.97, A:L.98 Water bridges: B:H.398, B:H.398 C8E.23: 9 residues within 4Å: Chain B: S.210, A.213, E.214 Chain E: L.61 Chain F: K.216, I.217, G.219, D.222 Ligands: C8E.103 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.217 C8E.42: 28 residues within 4Å: Chain B: P.97, L.98 Chain C: F.204, F.385, E.389, H.393, L.394, H.398, I.432, N.433, L.435, A.436, L.439, L.440, V.446, V.447, R.449, T.451, F.458, D.622, V.623, L.625, A.626, L.627, L.629, L.630, I.696 Ligands: FE2.41 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.440, C:L.625, C:A.626, C:L.629, C:L.630, B:P.97, B:L.98 Water bridges: C:H.398, C:H.398 C8E.43: 9 residues within 4Å: Chain C: S.210, A.213, E.214 Chain D: L.61 Chain E: K.216, I.217, G.219, D.222 Ligands: C8E.83 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.217 C8E.62: 28 residues within 4Å: Chain D: F.204, F.385, E.389, H.393, L.394, H.398, I.432, N.433, L.435, A.436, L.439, L.440, V.446, V.447, R.449, T.451, F.458, D.622, V.623, L.625, A.626, L.627, L.629, L.630, I.696 Chain F: P.97, L.98 Ligands: FE2.61 9 PLIP interactions: 2 interactions with chain F, 7 interactions with chain D Hydrophobic interactions: F:P.97, F:L.98, D:L.440, D:L.625, D:A.626, D:L.629, D:L.630 Water bridges: D:H.398, D:H.398 C8E.63: 9 residues within 4Å: Chain A: K.216, I.217, G.219, D.222 Chain C: L.61 Chain D: S.210, A.213, E.214 Ligands: C8E.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.217 Hydrogen bonds: D:E.214 C8E.82: 28 residues within 4Å: Chain D: P.97, L.98 Chain E: F.204, F.385, E.389, H.393, L.394, H.398, I.432, N.433, L.435, A.436, L.439, L.440, V.446, V.447, R.449, T.451, F.458, D.622, V.623, L.625, A.626, L.627, L.629, L.630, I.696 Ligands: FE2.81 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:L.440, E:L.625, E:A.626, E:L.629, E:L.630, D:P.97, D:L.98 Water bridges: E:H.398, E:H.398 C8E.83: 9 residues within 4Å: Chain B: L.61 Chain C: K.216, I.217, G.219, D.222 Chain E: S.210, A.213, E.214 Ligands: C8E.43 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:I.217 Hydrogen bonds: E:E.214 C8E.102: 28 residues within 4Å: Chain E: P.97, L.98 Chain F: F.204, F.385, E.389, H.393, L.394, H.398, I.432, N.433, L.435, A.436, L.439, L.440, V.446, V.447, R.449, T.451, F.458, D.622, V.623, L.625, A.626, L.627, L.629, L.630, I.696 Ligands: FE2.101 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:L.440, F:L.625, F:A.626, F:L.629, F:L.630, E:P.97, E:L.98 Water bridges: F:H.398, F:H.398 C8E.103: 9 residues within 4Å: Chain A: L.61 Chain B: K.216, I.217, G.219, D.222 Chain F: S.210, A.213, E.214 Ligands: C8E.23 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:E.214 Hydrophobic interactions: B:I.217

72 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: R.25, R.27, H.121 Ligand excluded by PLIP SO4.5: 1 residues within 4Å: Chain A: R.481 Ligand excluded by PLIP SO4.6: 7 residues within 4Å: Chain A: K.218, R.235, N.238 Chain D: K.218, R.235, N.238 Ligands: SO4.66 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: R.272, R.273, C.274, H.275, Y.276 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: S.316, G.317, A.331, A.332, L.353, S.354, Q.355 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: K.370, W.371, C.607 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain A: S.197, K.200, Y.428, G.635, D.636, R.638 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: G.31, E.32, A.33, F.108, R.110 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: D.369, K.370 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: Q.666, R.669 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: R.228, S.229, N.231, E.232 Chain D: K.234 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: Q.253, E.254, D.255, A.256 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: R.25, R.27, H.121 Ligand excluded by PLIP SO4.25: 1 residues within 4Å: Chain B: R.481 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain B: K.218, R.235, N.238 Chain F: K.218, R.235, N.238 Ligands: SO4.106 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain B: R.272, R.273, C.274, H.275, Y.276 Ligand excluded by PLIP SO4.28: 7 residues within 4Å: Chain B: S.316, G.317, A.331, A.332, L.353, S.354, Q.355 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: K.370, W.371, C.607 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain B: S.197, K.200, Y.428, G.635, D.636, R.638 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain B: G.31, E.32, A.33, F.108, R.110 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain B: D.369, K.370 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain B: Q.666, R.669 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain B: R.228, S.229, N.231, E.232 Chain F: K.234 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain B: Q.253, E.254, D.255, A.256 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain C: R.25, R.27, H.121 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Chain C: R.481 Ligand excluded by PLIP SO4.46: 7 residues within 4Å: Chain C: K.218, R.235, N.238 Chain E: K.218, R.235, N.238 Ligands: SO4.86 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain C: R.272, R.273, C.274, H.275, Y.276 Ligand excluded by PLIP SO4.48: 7 residues within 4Å: Chain C: S.316, G.317, A.331, A.332, L.353, S.354, Q.355 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain C: K.370, W.371, C.607 Ligand excluded by PLIP SO4.50: 6 residues within 4Å: Chain C: S.197, K.200, Y.428, G.635, D.636, R.638 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain C: G.31, E.32, A.33, F.108, R.110 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain C: D.369, K.370 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain C: Q.666, R.669 Ligand excluded by PLIP SO4.54: 5 residues within 4Å: Chain C: R.228, S.229, N.231, E.232 Chain E: K.234 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain C: Q.253, E.254, D.255, A.256 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain D: R.25, R.27, H.121 Ligand excluded by PLIP SO4.65: 1 residues within 4Å: Chain D: R.481 Ligand excluded by PLIP SO4.66: 7 residues within 4Å: Chain A: K.218, R.235, N.238 Chain D: K.218, R.235, N.238 Ligands: SO4.6 Ligand excluded by PLIP SO4.67: 5 residues within 4Å: Chain D: R.272, R.273, C.274, H.275, Y.276 Ligand excluded by PLIP SO4.68: 7 residues within 4Å: Chain D: S.316, G.317, A.331, A.332, L.353, S.354, Q.355 Ligand excluded by PLIP SO4.69: 3 residues within 4Å: Chain D: K.370, W.371, C.607 Ligand excluded by PLIP SO4.70: 6 residues within 4Å: Chain D: S.197, K.200, Y.428, G.635, D.636, R.638 Ligand excluded by PLIP SO4.71: 5 residues within 4Å: Chain D: G.31, E.32, A.33, F.108, R.110 Ligand excluded by PLIP SO4.72: 2 residues within 4Å: Chain D: D.369, K.370 Ligand excluded by PLIP SO4.73: 2 residues within 4Å: Chain D: Q.666, R.669 Ligand excluded by PLIP SO4.74: 5 residues within 4Å: Chain A: K.234 Chain D: R.228, S.229, N.231, E.232 Ligand excluded by PLIP SO4.75: 4 residues within 4Å: Chain D: Q.253, E.254, D.255, A.256 Ligand excluded by PLIP SO4.84: 3 residues within 4Å: Chain E: R.25, R.27, H.121 Ligand excluded by PLIP SO4.85: 1 residues within 4Å: Chain E: R.481 Ligand excluded by PLIP SO4.86: 7 residues within 4Å: Chain C: K.218, R.235, N.238 Chain E: K.218, R.235, N.238 Ligands: SO4.46 Ligand excluded by PLIP SO4.87: 5 residues within 4Å: Chain E: R.272, R.273, C.274, H.275, Y.276 Ligand excluded by PLIP SO4.88: 7 residues within 4Å: Chain E: S.316, G.317, A.331, A.332, L.353, S.354, Q.355 Ligand excluded by PLIP SO4.89: 3 residues within 4Å: Chain E: K.370, W.371, C.607 Ligand excluded by PLIP SO4.90: 6 residues within 4Å: Chain E: S.197, K.200, Y.428, G.635, D.636, R.638 Ligand excluded by PLIP SO4.91: 5 residues within 4Å: Chain E: G.31, E.32, A.33, F.108, R.110 Ligand excluded by PLIP SO4.92: 2 residues within 4Å: Chain E: D.369, K.370 Ligand excluded by PLIP SO4.93: 2 residues within 4Å: Chain E: Q.666, R.669 Ligand excluded by PLIP SO4.94: 5 residues within 4Å: Chain C: K.234 Chain E: R.228, S.229, N.231, E.232 Ligand excluded by PLIP SO4.95: 4 residues within 4Å: Chain E: Q.253, E.254, D.255, A.256 Ligand excluded by PLIP SO4.104: 3 residues within 4Å: Chain F: R.25, R.27, H.121 Ligand excluded by PLIP SO4.105: 1 residues within 4Å: Chain F: R.481 Ligand excluded by PLIP SO4.106: 7 residues within 4Å: Chain B: K.218, R.235, N.238 Chain F: K.218, R.235, N.238 Ligands: SO4.26 Ligand excluded by PLIP SO4.107: 5 residues within 4Å: Chain F: R.272, R.273, C.274, H.275, Y.276 Ligand excluded by PLIP SO4.108: 7 residues within 4Å: Chain F: S.316, G.317, A.331, A.332, L.353, S.354, Q.355 Ligand excluded by PLIP SO4.109: 3 residues within 4Å: Chain F: K.370, W.371, C.607 Ligand excluded by PLIP SO4.110: 6 residues within 4Å: Chain F: S.197, K.200, Y.428, G.635, D.636, R.638 Ligand excluded by PLIP SO4.111: 5 residues within 4Å: Chain F: G.31, E.32, A.33, F.108, R.110 Ligand excluded by PLIP SO4.112: 2 residues within 4Å: Chain F: D.369, K.370 Ligand excluded by PLIP SO4.113: 2 residues within 4Å: Chain F: Q.666, R.669 Ligand excluded by PLIP SO4.114: 5 residues within 4Å: Chain B: K.234 Chain F: R.228, S.229, N.231, E.232 Ligand excluded by PLIP SO4.115: 4 residues within 4Å: Chain F: Q.253, E.254, D.255, A.256 Ligand excluded by PLIP

12 x CA: CALCIUM ION(Non-covalent)

CA.16: 5 residues within 4Å: Chain A: G.35, G.37, T.38, D.105, A.106 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.35, A:G.37, A:D.105, A:A.106, H2O.2 CA.17: 5 residues within 4Å: Chain A: K.41, D.59, N.60, G.62, E.64 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:N.60, A:G.62, A:E.64, H2O.4 CA.36: 5 residues within 4Å: Chain B: G.35, G.37, T.38, D.105, A.106 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.35, B:G.37, B:D.105, B:A.106, H2O.16 CA.37: 5 residues within 4Å: Chain B: K.41, D.59, N.60, G.62, E.64 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:N.60, B:G.62, B:E.64, H2O.18 CA.56: 5 residues within 4Å: Chain C: G.35, G.37, T.38, D.105, A.106 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:G.35, C:G.37, C:D.105, C:A.106, H2O.30 CA.57: 5 residues within 4Å: Chain C: K.41, D.59, N.60, G.62, E.64 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.59, C:N.60, C:G.62, C:E.64, H2O.32 CA.76: 5 residues within 4Å: Chain D: G.35, G.37, T.38, D.105, A.106 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.35, D:G.37, D:D.105, D:A.106, H2O.44 CA.77: 5 residues within 4Å: Chain D: K.41, D.59, N.60, G.62, E.64 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.59, D:N.60, D:G.62, D:E.64, H2O.47 CA.96: 5 residues within 4Å: Chain E: G.35, G.37, T.38, D.105, A.106 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:G.35, E:G.37, E:D.105, E:A.106, H2O.58 CA.97: 5 residues within 4Å: Chain E: K.41, D.59, N.60, G.62, E.64 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.59, E:N.60, E:G.62, E:E.64, H2O.61 CA.116: 5 residues within 4Å: Chain F: G.35, G.37, T.38, D.105, A.106 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:G.35, F:G.37, F:D.105, F:A.106, H2O.72 CA.117: 5 residues within 4Å: Chain F: K.41, D.59, N.60, G.62, E.64 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.59, F:N.60, F:G.62, F:E.64, H2O.75

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 12 residues within 4Å: Chain A: H.573, A.574, S.577, A.578, L.630, S.631, K.632, E.633, L.689, I.690, E.691, I.696 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain A: F.212, K.216, L.221, D.222, R.449 Chain C: V.95, L.96, P.97 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain A: W.147, P.517, S.521, D.524 Ligand excluded by PLIP GOL.38: 12 residues within 4Å: Chain B: H.573, A.574, S.577, A.578, L.630, S.631, K.632, E.633, L.689, I.690, E.691, I.696 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain A: V.95, L.96, P.97 Chain B: F.212, K.216, L.221, D.222, R.449 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain B: W.147, P.517, S.521, D.524 Ligand excluded by PLIP GOL.58: 12 residues within 4Å: Chain C: H.573, A.574, S.577, A.578, L.630, S.631, K.632, E.633, L.689, I.690, E.691, I.696 Ligand excluded by PLIP GOL.59: 8 residues within 4Å: Chain B: V.95, L.96, P.97 Chain C: F.212, K.216, L.221, D.222, R.449 Ligand excluded by PLIP GOL.60: 4 residues within 4Å: Chain C: W.147, P.517, S.521, D.524 Ligand excluded by PLIP GOL.78: 12 residues within 4Å: Chain D: H.573, A.574, S.577, A.578, L.630, S.631, K.632, E.633, L.689, I.690, E.691, I.696 Ligand excluded by PLIP GOL.79: 8 residues within 4Å: Chain D: F.212, K.216, L.221, D.222, R.449 Chain F: V.95, L.96, P.97 Ligand excluded by PLIP GOL.80: 4 residues within 4Å: Chain D: W.147, P.517, S.521, D.524 Ligand excluded by PLIP GOL.98: 12 residues within 4Å: Chain E: H.573, A.574, S.577, A.578, L.630, S.631, K.632, E.633, L.689, I.690, E.691, I.696 Ligand excluded by PLIP GOL.99: 8 residues within 4Å: Chain D: V.95, L.96, P.97 Chain E: F.212, K.216, L.221, D.222, R.449 Ligand excluded by PLIP GOL.100: 4 residues within 4Å: Chain E: W.147, P.517, S.521, D.524 Ligand excluded by PLIP GOL.118: 12 residues within 4Å: Chain F: H.573, A.574, S.577, A.578, L.630, S.631, K.632, E.633, L.689, I.690, E.691, I.696 Ligand excluded by PLIP GOL.119: 8 residues within 4Å: Chain E: V.95, L.96, P.97 Chain F: F.212, K.216, L.221, D.222, R.449 Ligand excluded by PLIP GOL.120: 4 residues within 4Å: Chain F: W.147, P.517, S.521, D.524 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobe, M.J. et al., The structure of human 15-lipoxygenase-2 with a substrate mimic. J.Biol.Chem. (2014)

Release Date

2014-02-12

Peptides

Arachidonate 15-lipoxygenase B: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Arachidonate 15-lipoxygenase B

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