SMTL ID : 6sjo.1

Methyltransferase of the MtgA D102A mutant from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

1 x THH: N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID(Non-covalent)

THH.1: 15 residues within 4Å: Chain A: S.33, Y.36, R.37, D.76, N.130, V.153, D.195, A.225, S.227, N.228, Y.231, L.232, R.237, L.264, P.267 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.36 Hydrogen bonds: A:S.33, A:S.33, A:D.76, A:N.130, A:N.130, A:N.228 Water bridges: A:G.197, A:A.225, A:G.266 Salt bridges: A:D.195, A:R.237

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain B: S.33, D.76, L.78, N.130, A.225, L.264 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.33, B:N.130 GOL.3: 7 residues within 4Å: Chain B: N.130, L.155, F.157, D.195, G.197, A.225 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.130, B:V.198 Water bridges: B:D.195, B:G.197 GOL.4: 2 residues within 4Å: Chain B: K.40, D.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.40, B:D.51 GOL.5: 8 residues within 4Å: Chain B: D.13, I.14, N.15, Q.124, K.125, K.150, T.151, Q.191 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.15, B:T.151, B:Q.191, B:Q.191 Water bridges: B:D.13, B:D.13, B:K.150 GOL.6: 6 residues within 4Å: Chain B: K.4, F.5, T.6, A.7, Q.8, Q.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Badmann, T. et al., Structures in Tetrahydrofolate Methylation in Desulfitobacterial Glycine Betaine Metabolism at Atomic Resolution. Chembiochem (2020)

Release Date

2019-09-25

Peptides

Tetrahydromethanopterin S-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tetrahydromethanopterin S-methyltransferase