SMTL ID : 6sj8.1

Methyltransferase MtgA from Desulfitobacterium hafniense in complex with tetrahydrofolate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x 44V: (6S)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one(Non-covalent)

44V.1: 7 residues within 4Å: Chain A: N.130, V.153, L.155, D.195, A.225, N.228, L.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.130, A:N.130 Water bridges: A:G.197, A:A.225 Salt bridges: A:D.195 44V.6: 7 residues within 4Å: Chain B: N.130, V.153, L.155, D.195, A.225, L.264 Ligands: NA.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.130, B:N.130 Water bridges: B:G.197, B:A.225, B:N.228 Salt bridges: B:D.195

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

NA.2: 2 residues within 4Å: Chain A: Y.26, P.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.26 Water bridges: A:E.25 NA.7: 4 residues within 4Å: Chain B: F.157, G.197, V.198 Ligands: 44V.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.198, B:V.198 Water bridges: B:G.197

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: L.141, K.145, R.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.186 GOL.4: 5 residues within 4Å: Chain A: F.50, D.51, K.52, D.53 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.51, A:K.52, A:D.53, A:D.53 GOL.5: 5 residues within 4Å: Chain A: G.48, I.49, F.50, K.52 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.48, A:F.50, A:F.50 GOL.9: 3 residues within 4Å: Chain B: T.137, E.138, E.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.138, B:E.139 Water bridges: B:E.138 GOL.10: 5 residues within 4Å: Chain A: F.307 Chain B: D.200, V.201, L.232, W.233 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.201, B:A.229, B:L.232 Water bridges: B:D.200, B:A.202, B:K.234

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain B: E.138, L.141, A.142, R.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.186 Salt bridges: B:K.145

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

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