SMTL ID : 6lfe.1

Rat-COMT, Nitecapone,SAM and Mg bond

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

SAM.1: 24 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: EAO.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.70 Hydrogen bonds: A:N.43, A:V.44, A:Y.70, A:Y.73, A:S.74, 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 EAO: 3-(3,4-dihydroxy-5-nitrobenzylidene)pentane-2,4-dione(Non-covalent)

EAO.2: 13 residues within 4Å: Chain A: W.40, M.42, D.143, H.144, W.145, K.146, D.171, N.172, P.176, E.201 Ligands: SAM.1, MG.3, PEG.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.40, A:P.176 Hydrogen bonds: A:K.146, A:K.146, A:N.172, A:E.201

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.143, K.146, D.171, N.172 Ligands: SAM.1, EAO.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.143, A:D.171, H2O.1

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 6 residues within 4Å: Chain A: C.35, T.36, Q.37, K.38, E.39, W.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.35 IPA.5: 3 residues within 4Å: Chain A: A.98, Q.102, I.116 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.102, A:I.116 Water bridges: A:Q.102, A:I.116

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

PEG.6: 2 residues within 4Å: Chain A: W.145 Ligands: EAO.2 No protein-ligand interaction detected (PLIP) PEG.7: 4 residues within 4Å: Chain A: I.174, L.182, R.186, H.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.186, A:R.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iijima, H. et al., Crystal Structure of Catechol O-Methyltransferase Complexed with Nitecapone. Chem Pharm Bull (Tokyo) (2020)

Release Date

2020-03-04

Peptides

Catechol O-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Catechol O-methyltransferase

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