SMTL ID : 3tfi.1

DMSP-dependent demethylase from P. ubique - with substrate DMSP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x DQY: 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid(Non-covalent)

DQY.1: 5 residues within 4Å: Chain A: Y.32, L.37, W.197, P.234, S.246 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.32, A:W.197 Hydrogen bonds: A:S.246 Water bridges: A:Y.32, A:R.239, A:S.246, A:N.249 Salt bridges: A:R.239, B:R.11 DQY.4: 5 residues within 4Å: Chain B: Y.32, L.37, W.197, P.234, S.246 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.32, B:W.197 Water bridges: B:Y.32, B:Y.32, B:R.239, B:N.249 Salt bridges: A:R.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: D.125, S.126, Y.247 Chain B: R.13, H.34, D.127, I.129, F.130, E.147 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.125, A:Y.247, B:H.34 Water bridges: B:R.13, B:R.13, B:E.147 GOL.5: 8 residues within 4Å: Chain A: R.13, H.34, D.127, I.129, F.130, E.147 Chain B: S.126, Y.247 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.13, A:R.13 Hydrogen bonds: B:D.125

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

NA.3: 7 residues within 4Å: Chain A: T.15, L.36, L.37, D.59, V.60, A.61, A.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.59, A:A.62 NA.6: 7 residues within 4Å: Chain B: T.15, L.36, L.37, D.59, V.60, A.61, A.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.59, B:A.62 Water bridges: B:T.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schuller, D.J. et al., Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique. Protein Sci. (2012)

Release Date

2011-12-28

Peptides

GcvT-like Aminomethyltransferase protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GcvT-like Aminomethyltransferase protein

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