SMTL ID : 4kvl.1

Crystal structure of Oryza sativa fatty acid alpha-dioxygenase Y379F with palmitic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 23 residues within 4Å: Chain A: A.152, I.155, Q.156, V.159, M.163, D.164, H.165, N.263, W.265, T.379, F.382, R.383, M.384, H.385, I.419, F.456, L.459, I.473, L.475, L.478, R.482, R.486 Ligands: IMD.5 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:I.155, A:I.155, A:Q.156, A:Q.156, A:V.159, A:W.265, A:T.379, A:F.382, A:F.382, A:M.384, A:I.419, A:I.419, A:F.456, A:F.456, A:L.459, A:I.473, A:L.475, A:L.478 Hydrogen bonds: A:M.163, A:H.165, A:R.383 Water bridges: A:R.469, A:R.469, A:R.486, A:R.486, A:R.486, A:R.486 Salt bridges: A:H.165, A:R.482, A:R.486 pi-Stacking: A:F.456 Metal complexes: A:H.385

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 17 residues within 4Å: Chain A: L.53, L.56, R.60, H.314, W.318, T.319, M.328, M.332, A.334, N.335, F.378, F.382, F.552, F.555, I.556, A.559, R.562 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.56, A:W.318, A:T.319, A:A.334, A:F.382, A:F.555, A:F.555 Salt bridges: A:H.314, A:R.562 PLM.4: 6 residues within 4Å: Chain A: G.352, G.353, P.354, I.355, L.356 Ligands: PGE.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.356, A:L.356 Hydrogen bonds: A:G.353, A:I.355, A:L.356

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.161, T.213, W.215, D.217, S.219 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.161, A:T.213, A:T.213, A:W.215, A:S.219

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 7 residues within 4Å: Chain A: Q.156, V.159, H.160, R.212, R.262, N.263 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.156 Water bridges: A:N.263

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.6: 9 residues within 4Å: Chain A: F.27, I.30, G.31, F.34, L.54, N.57, T.58 Ligands: BOG.10, PGE.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.34, A:F.34, A:L.54 Hydrogen bonds: A:F.27, A:G.31, A:N.57 BOG.10: 6 residues within 4Å: Chain A: N.57, R.60, T.61, P.354, I.355 Ligands: BOG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.57, A:R.60

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

1PE.7: 13 residues within 4Å: Chain A: N.42, H.45, Y.491, R.495, I.501, P.502, I.503, D.508, E.539, K.540, K.541, I.542, E.549 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.42 Water bridges: A:K.46, A:K.46, A:R.495, A:R.495, A:R.495, A:R.495

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

PGE.8: 6 residues within 4Å: Chain A: V.20, Y.66, E.493, R.496, R.497, F.499 No protein-ligand interaction detected (PLIP) PGE.9: 4 residues within 4Å: Chain A: R.593, K.609, S.611, Y.621 No protein-ligand interaction detected (PLIP) PGE.12: 7 residues within 4Å: Chain A: I.242, G.243, D.244, D.245, G.246, K.277, Y.600 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.277, A:Y.600 Water bridges: A:N.280, A:E.602 PGE.13: 4 residues within 4Å: Chain A: A.37, F.38, R.41 Ligands: BOG.6 No protein-ligand interaction detected (PLIP) PGE.14: 3 residues within 4Å: Chain A: I.351, G.352 Ligands: PGE.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.352 PGE.15: 3 residues within 4Å: Chain A: G.353 Ligands: PLM.4, PGE.14 No protein-ligand interaction detected (PLIP)

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

PG4.11: 12 residues within 4Å: Chain A: A.70, V.71, R.73, S.75, H.76, N.99, E.101, A.102, F.108, P.371, Y.372, S.373 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.71, A:S.75 Water bridges: A:V.71, A:S.74, A:G.103, A:F.108

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 3 residues within 4Å: Chain A: K.312, W.336, K.587 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: R.333, G.341, K.342 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, G. et al., Crystal structures of alpha-dioxygenase from Oryza sativa: Insights into substrate binding and activation by hydrogen peroxide. Protein Sci. (2013)

Release Date

2013-08-21

Peptides

Fatty acid alpha-oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Fatty acid alpha-oxidase