SMTL ID : 1nbh.1

Structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate, GNMT:SAM:Ace

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: Y.33, N.138, R.175, Y.194, Y.220, Y.242 Ligands: SAM.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.194 Hydrogen bonds: A:Y.33, A:Y.33, A:N.138, A:Y.220 Salt bridges: A:R.175 ACT.3: 8 residues within 4Å: Chain B: W.30, Y.33, N.138, R.175, Y.194, Y.220, Y.242 Ligands: SAM.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.30, B:Y.194 Hydrogen bonds: B:Y.33, B:N.138, B:Y.220 Salt bridges: B:R.175 ACT.5: 7 residues within 4Å: Chain C: Y.33, N.138, R.175, Y.194, Y.220, Y.242 Ligands: SAM.6 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.194 Hydrogen bonds: C:Y.33, C:N.138 Salt bridges: C:R.175 ACT.7: 8 residues within 4Å: Chain D: W.30, Y.33, N.138, R.175, Y.194, Y.220, Y.242 Ligands: SAM.8 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.30, D:Y.194 Hydrogen bonds: D:Y.33, D:N.138 Salt bridges: D:R.175

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 21 residues within 4Å: Chain A: Y.21, W.30, I.34, R.40, V.63, A.64, G.66, V.69, D.85, A.86, S.87, M.90, A.115, N.116, W.117, L.136, G.137, S.139, H.142, Y.194 Ligands: ACT.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.30 Hydrogen bonds: A:W.30, A:A.64, A:D.70, A:A.86, A:S.87, A:N.116, A:W.117, A:S.139, A:Y.194 Water bridges: A:D.70 Salt bridges: A:R.40 pi-Stacking: A:W.117, A:W.117, A:W.117 SAM.4: 22 residues within 4Å: Chain B: Y.21, W.30, I.34, R.40, V.63, A.64, G.66, V.69, D.85, A.86, S.87, M.90, A.115, N.116, W.117, L.136, G.137, S.139, H.142, L.143, Y.194 Ligands: ACT.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.30 Hydrogen bonds: B:W.30, B:A.64, B:D.70, B:A.86, B:S.87, B:N.116, B:W.117, B:S.139, B:Y.194 Water bridges: B:D.70 Salt bridges: B:R.40 pi-Stacking: B:W.117, B:W.117, B:W.117 SAM.6: 22 residues within 4Å: Chain C: Y.21, W.30, I.34, R.40, V.63, A.64, G.66, V.69, D.70, D.85, A.86, S.87, M.90, A.115, N.116, W.117, L.136, G.137, S.139, H.142, Y.194 Ligands: ACT.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.30 Hydrogen bonds: C:W.30, C:A.64, C:A.86, C:S.87, C:N.116, C:W.117, C:S.139 Water bridges: C:D.70 Salt bridges: C:R.40 pi-Stacking: C:W.117, C:W.117, C:W.117 SAM.8: 21 residues within 4Å: Chain D: Y.21, W.30, I.34, R.40, V.63, A.64, G.66, V.69, D.85, A.86, S.87, M.90, A.115, N.116, W.117, L.136, G.137, S.139, H.142, Y.194 Ligands: ACT.7 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.30 Hydrogen bonds: D:W.30, D:A.64, D:A.86, D:S.87, D:N.116, D:W.117, D:S.139 Salt bridges: D:R.40 pi-Stacking: D:W.117, D:W.117, D:W.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takata, Y. et al., Catalytic mechanism of glycine N-methyltransferase. Biochemistry (2003)

Release Date

2003-03-04

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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