SMTL ID : 4hhr.1

Crystal Structure of fatty acid alpha-dioxygenase (Arabidopsis thaliana)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: I.170, Q.171, I.174, I.178, D.179, H.180, N.279, W.281, T.395, Y.398, R.399, M.400, H.401, L.404, I.435, W.471, I.475, L.491, L.494, R.498, R.502 Ligands: IMD.2 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:I.170, A:I.170, A:Q.171, A:Q.171, A:I.174, A:N.279, A:W.281, A:T.395, A:M.400, A:I.435, A:W.471, A:L.491, A:L.491, A:L.494 Hydrogen bonds: A:I.178, A:H.180 Water bridges: A:R.399, A:R.485, A:R.485, A:R.502, A:R.502, A:R.502 Salt bridges: A:H.180, A:R.399, A:R.498, A:R.502 Metal complexes: A:H.401

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 7 residues within 4Å: Chain A: Q.171, I.174, H.175, R.227, R.278, N.279 Ligands: HEM.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.171, A:R.278 Water bridges: A:R.227, A:N.279

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 5 residues within 4Å: Chain A: D.176, T.228, W.230, D.232, S.234 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:T.228, A:W.230, A:S.234 CA.4: 2 residues within 4Å: Chain A: E.530, E.533 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.530, A:E.533, H2O.10 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: D.306, D.308 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.306, A:D.308, H2O.14 CA.7: 1 residues within 4Å: Chain A: T.604 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.604, H2O.36 CA.8: 1 residues within 4Å: Chain A: D.634 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.634, H2O.4, H2O.7, H2O.15, H2O.24 CA.9: 1 residues within 4Å: Chain A: D.415 No protein-ligand interaction detected (PLIP) CA.10: 1 residues within 4Å: Chain A: D.618 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.618, H2O.17, H2O.24, H2O.28

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

CL.11: 4 residues within 4Å: Chain A: H.330, Y.398, F.571, R.578 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: K.328, W.352, N.603 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: N.240, T.243 Ligand excluded by PLIP

1 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.14: 9 residues within 4Å: Chain A: I.49, V.53, V.57, L.62, P.63, L.66, T.69, Y.70, V.73 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.49, A:T.69, A:V.73

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.15: 8 residues within 4Å: Chain A: R.511, I.517, P.518, I.519, E.523, D.524, E.555, K.556 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.511, A:T.520, A:D.524, A:E.555, A:K.557

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

PGE.16: 4 residues within 4Å: Chain A: E.600, W.601, T.604, R.614 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.600 Water bridges: A:R.614 PGE.17: 3 residues within 4Å: Chain A: L.355, L.356, Y.646 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.359 PGE.18: 6 residues within 4Å: Chain A: K.340, T.341, D.342, L.345, E.627, R.648 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.342 Water bridges: A:K.340, A:R.648, A:R.648

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goulah, C.C. et al., The crystal structure of alpha-Dioxygenase provides insight into diversity in the cyclooxygenase-peroxidase superfamily. Biochemistry (2013)

Release Date

2013-02-20

Peptides

Alpha-dioxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-dioxygenase

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