SMTL ID : 5gm2.3 (2 other biounits)

Crystal structure of methyltransferase TleD complexed with SAH and teleocidin A1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: G.85, C.86, G.87, T.91, A.107, V.108, Q.112, A.134, D.135, A.136, M.137, I.152, S.154, H.157, M.158 Chain B: V.17, Y.21, V.36, H.37 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.85, A:G.87, A:T.91, A:V.108, A:Q.112, A:Q.112, A:D.135, A:A.136, B:V.36 Salt bridges: B:H.37 SAH.3: 16 residues within 4Å: Chain A: V.36, H.37 Chain B: G.85, C.86, G.87, A.107, V.108, Q.112, A.134, D.135, A.136, I.152, E.153, S.154, H.157, M.158 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.85, B:G.87, B:V.108, B:Q.112, B:Q.112, B:D.135, B:D.135, B:A.136, B:I.152, A:V.36 Hydrophobic interactions: A:V.36 Salt bridges: A:H.37 SAH.5: 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: A.14, V.17, Y.21, V.36, H.37 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.85, C:G.87, C:T.91, C:V.108, C:S.109, C:Q.112, C:Q.112, C:D.135, C:A.136, C:I.152, D:V.36 Hydrophobic interactions: D:V.36 Salt bridges: D:H.37 SAH.7: 20 residues within 4Å: Chain C: V.17, Y.21, V.36, H.37 Chain D: G.85, C.86, G.87, T.91, 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: 3 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:V.36 Hydrogen bonds: C:V.36, D:G.87, D:T.91, D:V.108, D:Q.112, D:Q.112, D:D.135, D:D.135, D:A.136, D:I.152 Salt bridges: C:H.37 SAH.9: 21 residues within 4Å: Chain E: 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 F: V.17, Y.21, V.36, H.37 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain F Hydrogen bonds: 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, F:V.36 Hydrophobic interactions: F:V.36 Salt bridges: F:H.37 SAH.11: 17 residues within 4Å: Chain E: S.35, V.36, H.37 Chain F: G.85, C.86, G.87, T.91, V.108, Q.112, A.134, D.135, A.136, I.152, E.153, S.154, H.157, M.158 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.85, F:G.87, F:T.91, F:V.108, F:Q.112, F:Q.112, F:D.135, F:D.135, F:A.136, E:V.36 Water bridges: F:I.152 Salt bridges: E:H.37

6 x TEX: (2S,5S)-9-[(3R)-3,7-dimethylocta-1,6-dien-3-yl]-5-(hydroxymethyl)-1-methyl-2-(propan-2-yl)-1,2,4,5,6,8-hexahydro-3H-[1,4]diazonino[7,6,5-cd]indol-3-one(Non-covalent)

TEX.2: 19 residues within 4Å: Chain A: E.153, C.156, H.157, L.180, E.181, S.182, F.196, Y.200, L.232, T.235, M.236, L.273, F.279 Chain B: Y.21, Y.28, L.32, V.36, H.37, C.38 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:Y.28, B:L.32, A:F.196, A:Y.200, A:L.232, A:T.235, A:L.273, A:F.279 Hydrogen bonds: A:E.153, A:C.156, A:S.182 pi-Stacking: A:Y.200 TEX.4: 17 residues within 4Å: Chain A: Y.28, L.32, H.37, C.38 Chain B: E.153, C.156, H.157, L.180, E.181, S.182, F.196, Y.200, L.232, T.235, M.236, L.273, F.279 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.196, B:Y.200, B:L.232, B:T.235, B:L.273, B:F.279, A:Y.28, A:L.32 Hydrogen bonds: B:E.153, B:C.156, B:S.182 pi-Stacking: B:Y.200 TEX.6: 20 residues within 4Å: Chain C: E.153, C.156, H.157, L.180, E.181, S.182, F.196, Y.200, P.205, L.232, T.235, M.236, L.273, F.279 Chain D: Y.21, Y.28, L.32, V.36, H.37, C.38 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.196, C:L.232, C:L.232, C:T.235, C:L.273, C:F.279, D:Y.28, D:L.32, D:V.36 Hydrogen bonds: C:E.153, C:C.156, C:E.181, C:S.182 pi-Stacking: C:Y.200 TEX.8: 19 residues within 4Å: Chain C: Y.21, Y.28, L.32, V.36, H.37, C.38 Chain D: E.153, C.156, H.157, L.180, E.181, S.182, F.196, Y.200, L.232, T.235, M.236, L.273, F.279 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.196, D:Y.200, D:L.232, D:L.232, D:T.235, D:L.273, D:F.279, C:Y.28, C:L.32 Hydrogen bonds: D:E.153, D:C.156, D:E.181, D:S.182 pi-Stacking: D:Y.200 TEX.10: 19 residues within 4Å: Chain E: E.153, C.156, H.157, L.180, E.181, S.182, F.196, Y.200, L.232, T.235, M.236, L.273, F.279 Chain F: Y.21, Y.28, L.32, V.36, H.37, C.38 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain E Hydrophobic interactions: F:Y.28, F:L.32, E:F.196, E:L.232, E:L.232, E:T.235, E:L.273, E:F.279 Hydrogen bonds: E:E.153, E:C.156, E:E.181, E:S.182 pi-Stacking: E:Y.200 TEX.12: 19 residues within 4Å: Chain E: Y.28, L.32, H.37, C.38 Chain F: E.153, C.156, H.157, L.180, E.181, S.182, F.196, Y.200, P.205, L.232, T.235, M.236, L.273, T.277, F.279 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.196, F:L.232, F:L.232, F:T.235, F:L.273, F:F.279, E:L.32 Hydrogen bonds: F:E.153, F:C.156, F:L.180, F:S.182 pi-Stacking: F:Y.200

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
M

B
N

C
O

D
P

E
Q

F
R

O-methylransferase

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