SMTL ID : 3thr.1

Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x C2F: 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID(Non-covalent)

C2F.1: 17 residues within 4Å: Chain A: Y.6, R.7, T.8 Chain B: S.206, L.208, H.215, M.216, T.218, R.240 Chain C: S.4, V.5, Y.6 Chain D: D.146, S.147, L.208, H.215, M.216 15 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A, 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: B:T.218, A:Y.6, A:Y.6, D:L.208 Hydrogen bonds: B:H.215, B:T.218, B:R.240, B:R.240, A:Y.6 Water bridges: B:S.206, B:S.206, B:T.218, C:S.4 pi-Cation interactions: B:R.240 Salt bridges: D:H.215 C2F.3: 4 residues within 4Å: Chain B: K.191, Y.280, V.281, C.283 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.191, B:V.281, B:V.281, B:V.281 C2F.4: 6 residues within 4Å: Chain C: R.60, P.126, A.127, G.128, G.130, F.131 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:P.126 Hydrogen bonds: C:R.60, C:R.60, C:G.130 Water bridges: C:S.81, C:T.83, C:D.129, C:D.129, C:D.129, C:D.129 pi-Cation interactions: C:R.60 C2F.6: 14 residues within 4Å: Chain A: L.208, H.215, M.216 Chain B: S.4, V.5, Y.6 Chain C: L.208, H.215, M.216, T.218, R.240 Chain D: Y.6, R.7, T.8 13 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A, 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:T.218, D:Y.6, D:Y.6 Hydrogen bonds: C:H.215, C:T.218, C:T.218, C:R.240, C:R.240, D:Y.6, B:S.4 Water bridges: C:S.206, C:S.206 Salt bridges: A:H.215

3 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.2: 14 residues within 4Å: Chain A: W.31, Y.34, I.35, T.38, M.91, L.137, G.138, N.139, S.140, H.143, L.241 Chain B: A.14, A.15, E.16 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.34, A:Y.34, A:Y.34, A:G.138, B:A.14 Water bridges: A:Y.243 TAM.5: 12 residues within 4Å: Chain C: W.31, Y.34, I.35, T.38, T.68, M.91, G.138, N.192, L.241 Chain D: A.14, A.15, E.16 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.34 Hydrogen bonds: C:T.68, C:G.138, C:N.192, D:A.14, D:E.16 Water bridges: C:T.38, D:E.16 TAM.7: 6 residues within 4Å: Chain C: E.16 Chain D: Y.34, I.35, M.91, G.138, N.192 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.34, D:Y.34, D:N.192 Water bridges: D:H.143, D:K.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luka, Z. et al., Differences in folate-protein interactions result in differing inhibition of native rat liver and recombinant glycine N-methyltransferase by 5-methyltetrahydrofolate. Biochim.Biophys.Acta (2011)

Release Date

2011-11-16

Peptides

Glycine N-methyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycine N-methyltransferase

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