SMTL ID : 5o7y.1

Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum in complex with succinate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 6 residues within 4Å: Chain A: H.241, D.243, H.298 Ligands: SIN.2, EDO.3, EDO.18 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.241, A:D.243, A:H.298

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 12 residues within 4Å: Chain A: N.224, Y.226, L.238, H.241, L.250, L.259, H.298, R.308, S.310 Ligands: NI.1, EDO.3, EDO.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.238, A:L.250 Hydrogen bonds: A:N.224, A:S.310 Salt bridges: A:H.241, A:H.298, A:R.308

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

EDO.3: 7 residues within 4Å: Chain A: H.241, D.243, F.314 Ligands: NI.1, SIN.2, EDO.18, PEG.21 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: P.59, V.60, I.61, R.80 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: K.75, L.78, D.79, H.82, A.199 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: F.113, E.120, K.121, T.122, K.123, Y.124, K.169 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: I.287, I.323, G.324, K.339, S.340, G.341, S.342, L.347, M.365 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: K.208, V.322, I.323, G.324, S.340, G.341 Ligands: EDO.16 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: L.159 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: K.123, S.168, K.169, L.170, P.171 Ligands: EDO.19 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: H.96, G.97, E.184, K.187, V.191 Ligands: EDO.17 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: L.76, D.79, R.80, F.83 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: Q.126, F.134, G.135, Q.136, G.137, F.138 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: V.60, D.62, V.94, N.95 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: M.4, K.8 Ligand excluded by PLIP EDO.16: 10 residues within 4Å: Chain A: K.208, G.209, V.213, M.288, V.322, I.323, G.324, P.325, I.326 Ligands: EDO.8 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: G.97, E.184 Ligands: EDO.11 Ligand excluded by PLIP EDO.18: 10 residues within 4Å: Chain A: F.90, D.243, T.248, L.250, L.259, N.280, H.298 Ligands: NI.1, SIN.2, EDO.3 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: V.172 Ligands: EDO.10 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 3 residues within 4Å: Chain A: S.327, S.328, I.330 No protein-ligand interaction detected (PLIP) PEG.21: 10 residues within 4Å: Chain A: D.243, F.244, G.245, G.246, L.247, T.248, F.314, H.315, D.316 Ligands: EDO.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.244, A:G.245, A:G.246, A:H.315, A:H.315, A:D.316 Water bridges: A:R.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kluza, A. et al., Crystal structure of thebaine 6-O-demethylase from the morphine biosynthesis pathway. J. Struct. Biol. (2018)

Release Date

2018-02-14

Peptides

Thebaine 6-O-demethylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thebaine 6-O-demethylase

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