SMTL ID : 4ymg.1

Crystal structure of SAM-bound Podospora anserina methyltransferase PaMTH1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 20 residues within 4Å: Chain A: K.47, M.48, S.49, G.73, C.74, Y.75, Y.78, S.79, E.98, Y.99, S.100, G.125, P.126, A.127, E.128, D.144, A.145, N.146, Y.153 Ligands: PO4.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.75 Hydrogen bonds: A:S.49, A:Y.75, A:S.79, A:S.79, A:S.79, A:Y.99, A:A.127, A:E.128, A:D.144, A:N.146, A:Y.153 Water bridges: A:K.47, A:N.146 Salt bridges: A:D.144 pi-Stacking: A:Y.99, A:Y.99 SAM.6: 20 residues within 4Å: Chain B: K.47, M.48, S.49, G.73, C.74, Y.75, Y.78, S.79, E.98, Y.99, S.100, G.125, P.126, A.127, E.128, D.144, A.145, N.146, Y.153 Ligands: PO4.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.75 Hydrogen bonds: B:S.49, B:Y.75, B:S.79, B:S.79, B:S.79, B:Y.99, B:A.127, B:E.128, B:D.144, B:N.146, B:Y.153 Water bridges: B:K.47, B:C.74, B:Y.99 Salt bridges: B:D.144 pi-Stacking: B:Y.99, B:Y.99

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: Y.84, K.91, G.117, R.119 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.84, A:G.117 Water bridges: A:G.117 Salt bridges: A:K.91, A:R.119 PO4.3: 6 residues within 4Å: Chain A: K.47, A.145, N.146, K.147, Y.196 Ligands: SAM.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.196 Water bridges: A:K.47, A:K.47, A:K.147, A:K.147, A:K.147 Salt bridges: A:K.47, A:K.147 PO4.7: 4 residues within 4Å: Chain B: K.47, N.146, Y.196 Ligands: SAM.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.196, B:Y.196 Water bridges: B:K.47, B:K.47, B:Y.196, B:Y.196 Salt bridges: B:K.47

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 7 residues within 4Å: Chain A: D.63, R.64, N.166 Chain B: D.63, R.64, N.166 Ligands: MG.5 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 1 residues within 4Å: Ligands: PG4.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chatterjee, D. et al., Structure and Biophysical Characterization of the S-Adenosylmethionine-dependent O-Methyltransferase PaMTH1, a Putative Enzyme Accumulating during Senescence of Podospora anserina. J.Biol.Chem. (2015)

Release Date

2015-05-27

Peptides

Putative SAM-dependent O-methyltranferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative SAM-dependent O-methyltranferase

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