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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

monomer

Ligands

1 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

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

C8E.2: 26 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 Ligands: FE2.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.440, A:L.625, A:A.626, A:L.629, A:L.630 Water bridges: A:H.398, A:H.398 C8E.3: 3 residues within 4Å: Chain A: S.210, A.213, E.214 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: R.25, R.27, H.121 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.25, A:R.27, A:H.121 SO4.5: 1 residues within 4Å: Chain A: R.481 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.481 SO4.6: 3 residues within 4Å: Chain A: K.218, R.235, N.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.238 Salt bridges: A:K.218, A:R.235 SO4.7: 5 residues within 4Å: Chain A: R.272, R.273, C.274, H.275, Y.276 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.275, A:Y.276, A:Y.276 Water bridges: A:R.272, A:R.272 Salt bridges: A:R.272 SO4.8: 7 residues within 4Å: Chain A: S.316, G.317, A.331, A.332, L.353, S.354, Q.355 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.316, A:G.317, A:A.332, A:Q.355 Water bridges: A:I.318 SO4.9: 3 residues within 4Å: Chain A: K.370, W.371, C.607 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.371 Salt bridges: A:K.370 SO4.10: 6 residues within 4Å: Chain A: S.197, K.200, Y.428, G.635, D.636, R.638 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.197, A:Y.428, A:D.636 Water bridges: A:K.200, A:K.200 Salt bridges: A:K.200, A:R.638 SO4.11: 5 residues within 4Å: Chain A: G.31, E.32, A.33, F.108, R.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.32, A:A.33, A:R.110 Water bridges: A:D.645 SO4.12: 2 residues within 4Å: Chain A: D.369, K.370 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.370 SO4.13: 2 residues within 4Å: Chain A: Q.666, R.669 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.666 Salt bridges: A:R.669 SO4.14: 4 residues within 4Å: Chain A: R.228, S.229, N.231, E.232 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.228, A:S.229, A:N.231 Water bridges: A:S.229 SO4.15: 4 residues within 4Å: Chain A: Q.253, E.254, D.255, A.256 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.253, A:D.255 Water bridges: A:D.255, A:D.255

2 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

3 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.577, A:E.633, A:E.633 Water bridges: A:H.573, A:H.573, A:A.574, A:L.689, A:E.691 GOL.19: 5 residues within 4Å: Chain A: F.212, K.216, L.221, D.222, R.449 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.216, A:D.222 Water bridges: A:L.221 GOL.20: 4 residues within 4Å: Chain A: W.147, P.517, S.521, D.524 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.524

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Arachidonate 15-lipoxygenase B

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