SMTL ID : 6sjn.1

Methyltransferase MtgA from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate (P212121)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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: 16 residues within 4Å: Chain A: S.33, Y.36, R.37, D.76, D.103, N.130, V.153, D.195, A.225, S.227, N.228, Y.231, L.232, R.237, L.264, P.267 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.36, A:P.267 Hydrogen bonds: A:S.33, A:S.33, A:D.103, A:N.130, A:N.130, A:S.227, A:N.228 Water bridges: A:R.37, A:R.37, A:V.198, A:V.198, A:A.225, A:Y.231, A:G.266 Salt bridges: A:D.103, A:D.195, A:R.237

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.3: 5 residues within 4Å: Chain B: L.58, Q.61, E.62, M.268, A.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.268

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain B: K.40, I.41, D.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.40 Water bridges: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.15, B:T.151, B:Q.191, B:Q.191 Water bridges: B:D.13, B:K.150 GOL.6: 4 residues within 4Å: Chain B: Y.136, T.137, E.138 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.138, B:E.138 GOL.7: 5 residues within 4Å: Chain B: K.4, T.6, A.7, Q.8, Q.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.22 Water bridges: B:A.7, B:Q.8 GOL.8: 4 residues within 4Å: Chain B: T.137, E.138, E.139 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.138, B:E.139 Water bridges: B:E.139

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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