SMTL ID : 5gm1.1 (2 other biounits)

Crystal structure of methyltransferase TleD complexed with SAH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

7 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 22 residues within 4Å: Chain A: G.85, C.86, G.87, T.91, V.106, A.107, V.108, Q.112, A.134, D.135, A.136, M.137, I.152, E.153, S.154, H.157, M.158 Chain B: V.17, Y.21, S.35, V.36, H.37 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.85, A:G.87, A:T.91, A:V.108, A:S.109, A:Q.112, A:Q.112, A:D.135, A:D.135, A:A.136, B:V.36 Water bridges: A:I.152 Hydrophobic interactions: B:V.36 Salt bridges: B:H.37 SAH.2: 23 residues within 4Å: Chain A: V.17, Y.21, S.35, V.36, H.37 Chain B: G.85, C.86, G.87, T.91, V.106, A.107, V.108, S.109, Q.112, A.134, D.135, A.136, M.137, I.152, E.153, S.154, H.157, M.158 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.85, B:G.87, B:T.91, B:V.108, B:S.109, B:Q.112, B:Q.112, B:D.135, B:D.135, B:A.136, B:I.152, A:V.36 Water bridges: B:I.152 Hydrophobic interactions: A:V.36 Salt bridges: A:H.37 SAH.3: 4 residues within 4Å: Chain A: Y.244, S.245 Chain B: Y.244, S.245 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.244 Hydrogen bonds: A:Y.244 SAH.4: 23 residues within 4Å: Chain C: G.85, C.86, G.87, T.91, V.106, A.107, V.108, S.109, Q.112, A.134, D.135, A.136, M.137, I.152, E.153, S.154, H.157, M.158 Chain D: V.17, Y.21, S.35, V.36, H.37 13 PLIP interactions: 3 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:V.36 Hydrogen bonds: D:V.36, C:G.85, C:G.87, C:V.108, C:S.109, C:Q.112, C:Q.112, C:D.135, C:A.136, C:I.152 Salt bridges: D:H.37 Water bridges: C:I.152 SAH.5: 22 residues within 4Å: Chain C: V.17, Y.21, V.36, H.37 Chain D: G.85, C.86, G.87, T.91, V.106, A.107, V.108, S.109, Q.112, A.134, D.135, A.136, M.137, I.152, E.153, S.154, H.157, M.158 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.87, D:T.91, D:V.108, D:S.109, D:Q.112, D:Q.112, D:D.135, D:A.136, D:I.152, D:I.152, C:V.36 Hydrophobic interactions: C:V.36 Salt bridges: C:H.37 SAH.6: 21 residues within 4Å: Chain E: G.85, C.86, G.87, T.91, A.107, V.108, S.109, Q.112, A.134, D.135, A.136, M.137, I.152, E.153, S.154, H.157, M.158 Chain F: V.17, Y.21, V.36, H.37 14 PLIP interactions: 4 interactions with chain F, 10 interactions with chain E Hydrophobic interactions: F:V.36 Hydrogen bonds: F:V.36, E:G.85, E:G.87, E:T.91, E:V.108, E:S.109, E:Q.112, E:Q.112, E:D.135, E:A.136 Water bridges: F:S.35, E:G.89 Salt bridges: F:H.37 SAH.7: 22 residues within 4Å: Chain E: V.17, Y.21, S.35, V.36, H.37 Chain F: G.85, C.86, G.87, T.91, V.106, A.107, V.108, Q.112, A.134, D.135, A.136, M.137, I.152, E.153, S.154, H.157, M.158 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:G.85, F:G.87, F:V.108, F:S.109, F:Q.112, F:Q.112, F:D.135, F:A.136, E:V.36 Water bridges: F:I.152 Hydrophobic interactions: E:V.36 Salt bridges: E:H.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, F. et al., Crystal structure and enantioselectivity of terpene cyclization in SAM-dependent methyltransferase TleD. Biochem.J. (2016)

Release Date

2016-09-28

Peptides

O-methylransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

O-methylransferase

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