SMTL ID : 4wfo.1

manganese-substituted soybean lipoxygenase-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: H.518, H.523, H.709, N.713, I.856, I.858 Ligands: EDO.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.518, A:H.523, A:H.709, H2O.12

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

EDO.2: 9 residues within 4Å: Chain A: V.145, F.163, A.164, N.165, H.166, T.167, V.539, L.540, K.545 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.166, A:K.545 Water bridges: A:H.166 EDO.3: 5 residues within 4Å: Chain A: D.310, G.314, G.315, I.316, K.317 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.310, A:G.314, A:K.317 Water bridges: A:D.310, A:K.317 EDO.4: 6 residues within 4Å: Chain A: I.431, P.434, Y.435, M.585, A.588, V.589 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.588, A:A.588 EDO.5: 12 residues within 4Å: Chain A: W.359, M.360, F.365, L.499, K.502, A.503, I.506, M.724, N.725, R.726, P.727, Y.753 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.359 EDO.6: 8 residues within 4Å: Chain A: A.404, D.405, L.407, L.409, Y.412, T.413, M.414 Ligands: ACT.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.414 EDO.7: 8 residues within 4Å: Chain A: N.209, G.242, P.243, T.244, P.248, N.249, T.250, E.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.209, A:N.249 EDO.8: 11 residues within 4Å: Chain A: Q.514, L.515, H.518, W.519, H.523, L.565, I.566, I.572, L.773, I.858 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.514, A:W.519 Water bridges: A:Q.514, A:H.518, A:I.858, A:I.858 EDO.9: 5 residues within 4Å: Chain A: H.166, T.167, Y.168, S.793, D.794 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.167, A:D.794 Water bridges: A:D.794, A:D.794

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 9 residues within 4Å: Chain A: D.459, G.460, T.461, D.626, S.823, L.824, G.826, N.827, R.828 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.461 Hydrogen bonds: A:G.826, A:N.827 ACT.11: 3 residues within 4Å: Chain A: Y.336, R.337, T.338 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.338 Water bridges: A:R.337, A:R.337, A:R.337 Salt bridges: A:R.337 ACT.12: 9 residues within 4Å: Chain A: T.574, T.575, F.576, T.728, A.729, R.731, T.758, S.759, P.762 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.729, A:T.758, A:P.762 Hydrogen bonds: A:T.574 ACT.13: 7 residues within 4Å: Chain A: L.407, D.408, L.409, D.410, G.411, Y.412 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.409, A:G.411 ACT.14: 7 residues within 4Å: Chain A: F.305, H.309, Q.356, S.357, W.359, M.360, M.724 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.305 Hydrogen bonds: A:W.359 Salt bridges: A:H.309 ACT.15: 2 residues within 4Å: Chain A: V.245, K.252 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.215, A:D.215, A:K.252 Salt bridges: A:K.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carr, C.A.M. et al., Direct detection of active-site geometries in soybean lipoxygenase-1 by ENDOR. To Be Published

Release Date

2015-09-30

Peptides

Seed linoleate 13S-lipoxygenase-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Seed linoleate 13S-lipoxygenase-1