SMTL ID : 7xjb.3 (3 other biounits)

Rat-COMT, opicapone,SAM and Mg bond

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 23 residues within 4Å: Chain A: M.42, N.43, V.44, E.66, G.68, A.69, Y.70, Y.73, S.74, M.91, E.92, M.93, N.94, Y.97, G.119, A.120, S.121, Q.122, F.141, D.143, H.144, W.145 Ligands: DNI.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.70 Hydrogen bonds: A:N.43, A:V.44, A:E.66, A:Y.70, A:Y.73, A:S.74, A:S.74, A:M.93, A:S.121, A:Q.122, A:D.143, A:W.145 Water bridges: A:G.72, A:A.75, A:Q.122 Salt bridges: A:D.143 pi-Stacking: A:W.145

1 x DNI: Opicapone(Non-covalent)

DNI.2: 16 residues within 4Å: Chain A: W.40, M.42, K.48, D.143, H.144, W.145, K.146, D.171, N.172, V.175, P.176, L.200, E.201, M.203 Ligands: SAM.1, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.40, A:W.40, A:P.176, A:L.200, A:L.200 Hydrogen bonds: A:K.48, A:D.143, A:K.146, A:D.171, A:D.171, A:N.172

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.143, K.146, D.171, N.172 Ligands: DNI.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.143, A:D.171, H2O.1

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

CL.4: 3 residues within 4Å: Chain A: D.46, A.47, Y.202 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takebe, K. et al., Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O -Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses. J.Chem.Inf.Model. (2023)

Release Date

2023-05-31

Peptides

Catechol O-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Catechol O-methyltransferase

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