SMTL ID : 2yck.1

methyltransferase bound with tetrahydrofolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: S.8, H.9, M.10 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.10 Salt bridges: A:H.9 SO4.2: 3 residues within 4Å: Chain A: H.9, R.202 Ligands: SO4.1 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.202, A:R.202 Salt bridges: A:H.9, A:R.202 SO4.3: 3 residues within 4Å: Chain A: H.99, R.100, G.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.101 SO4.4: 2 residues within 4Å: Chain A: R.17, W.40 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.17 SO4.5: 4 residues within 4Å: Chain A: D.241, D.242, D.243, A.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.243, A:D.243, A:A.244 Water bridges: A:D.242 SO4.6: 4 residues within 4Å: Chain A: A.60, D.61, D.62, P.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.61 SO4.7: 1 residues within 4Å: Chain A: W.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.113 SO4.10: 4 residues within 4Å: Chain B: S.8, H.9, M.10 Ligands: SO4.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.10 Salt bridges: B:H.9 SO4.11: 3 residues within 4Å: Chain B: H.9, R.202 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.202, B:R.202 Salt bridges: B:H.9, B:R.202 SO4.12: 3 residues within 4Å: Chain B: H.99, R.100, G.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.101 SO4.13: 2 residues within 4Å: Chain B: R.17, W.40 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.17 SO4.14: 4 residues within 4Å: Chain B: D.241, D.242, D.243, A.244 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.242, B:D.243, B:D.243, B:D.243, B:A.244 Water bridges: B:D.242 SO4.15: 4 residues within 4Å: Chain B: A.60, D.61, D.62, P.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.61 SO4.16: 1 residues within 4Å: Chain B: W.113 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.113

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: P.81, G.101, H.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.102 Water bridges: A:D.79, A:H.102 GOL.17: 3 residues within 4Å: Chain B: P.81, G.101, H.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.102 Water bridges: B:D.79, B:H.102

2 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)

THG.9: 15 residues within 4Å: Chain A: E.16, M.21, F.22, D.85, N.106, I.130, L.132, D.170, G.206, S.208, N.209, Q.212, K.213, R.217, I.237 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.22, A:F.22 Hydrogen bonds: A:M.21, A:D.85, A:N.106, A:N.106, A:G.206, A:N.209, A:N.209, A:Q.212, A:R.217, A:R.217 Water bridges: A:E.16, A:N.19, A:N.55, A:D.170, A:L.172, A:K.213, A:K.213 Salt bridges: A:D.170, A:K.213, A:R.217 THG.18: 15 residues within 4Å: Chain B: E.16, M.21, F.22, D.85, N.106, I.130, L.132, D.170, G.206, S.208, N.209, Q.212, K.213, R.217, I.237 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.22, B:F.22 Hydrogen bonds: B:M.21, B:D.85, B:N.106, B:N.106, B:G.206, B:N.209, B:N.209, B:Q.212, B:R.217, B:R.217 Water bridges: B:N.19, B:N.55, B:D.170, B:L.172, B:K.213, B:K.213 Salt bridges: B:D.170, B:K.213, B:R.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goetzl, S. et al., Structural Basis for Electron and Methyl-Group Transfer in a Methyltransferase System Operating in the Reductive Acetyl-Coa Pathway. J.Mol.Biol. (2011)

Release Date

2011-06-08

Peptides

5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE