SMTL ID : 5o9w.1

Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum in complex with 2-oxoglutarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.241, D.243, H.298 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.241, A:D.243, A:H.298, H2O.1

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 14 residues within 4Å: Chain A: R.222, N.224, Y.226, L.238, H.241, D.243, L.250, L.259, H.298, R.308, S.310, A.312, F.314 Ligands: NI.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.238, A:L.250 Hydrogen bonds: A:N.224, A:S.310 Water bridges: A:R.222 Salt bridges: A:R.222, A:H.241, A:R.308

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

EDO.3: 5 residues within 4Å: Chain A: K.75, L.78, D.79, H.82, A.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.75, A:L.78 EDO.4: 4 residues within 4Å: Chain A: P.59, V.60, I.61, R.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.60 Water bridges: A:I.58, A:V.60, A:D.62 EDO.5: 10 residues within 4Å: Chain A: I.287, I.323, G.324, K.339, S.340, G.341, S.342, L.347, M.365 Ligands: UNX.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.341, A:S.342, A:S.342 EDO.6: 2 residues within 4Å: Chain A: L.157, L.159 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: L.76, D.79, R.80, F.83 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.80 EDO.8: 6 residues within 4Å: Chain A: Q.126, F.134, G.135, Q.136, G.137, F.138 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.126, A:F.134, A:G.137 Water bridges: A:E.17, A:Q.126, A:D.130, A:Q.136 EDO.9: 3 residues within 4Å: Chain A: G.97, E.184 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.96, A:G.97, A:D.99 EDO.10: 8 residues within 4Å: Chain A: F.113, E.120, K.121, T.122, K.123, Y.124, L.166, K.169 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.120, A:K.123, A:Y.124 Water bridges: A:K.121, A:T.122, A:Y.124 EDO.11: 9 residues within 4Å: Chain A: K.208, G.209, V.213, M.288, V.322, I.323, G.324, P.325, I.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.208, A:V.322, A:G.324 Water bridges: A:S.327 EDO.12: 7 residues within 4Å: Chain A: H.96, G.97, V.98, E.184, K.187, L.188 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.184, A:L.188 EDO.13: 4 residues within 4Å: Chain A: V.60, D.62, V.94, N.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.62, A:N.95 Water bridges: A:V.60, A:D.62 EDO.14: 3 residues within 4Å: Chain A: M.4, A.7, K.8 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: A.25, K.26, T.28, P.228 No protein-ligand interaction detected (PLIP)

6 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.16: 5 residues within 4Å: Chain A: S.1, N.2, A.3, K.6 Ligands: UNX.17 No protein-ligand interaction detected (PLIP) UNX.17: 3 residues within 4Å: Chain A: K.6 Ligands: UNX.16, UNX.18 No protein-ligand interaction detected (PLIP) UNX.18: 2 residues within 4Å: Chain A: K.6 Ligands: UNX.17 No protein-ligand interaction detected (PLIP) UNX.19: 5 residues within 4Å: Chain A: K.339, S.340, S.342 Ligands: EDO.5, UNX.21 No protein-ligand interaction detected (PLIP) UNX.20: 4 residues within 4Å: Chain A: K.339, E.350, M.365 Ligands: UNX.21 No protein-ligand interaction detected (PLIP) UNX.21: 6 residues within 4Å: Chain A: K.339, S.342, L.347, E.350 Ligands: UNX.19, UNX.20 No protein-ligand interaction detected (PLIP)

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

PEG.22: 5 residues within 4Å: Chain A: V.131, E.132, M.153, F.155, A.220 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.131, A:G.135

1 x NA: SODIUM ION(Non-functional Binders)

NA.23: 2 residues within 4Å: Chain A: S.327, I.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.327

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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