SMTL ID : 5epe.1

Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-12-mer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.17 Hydrogen bonds: A:H.17, A:N.18, A:G.44, A:G.46, A:L.67, A:S.68, A:D.94, A:A.95 Water bridges: A:S.45, A:S.47, A:E.49, A:V.110 SAH.3: 19 residues within 4Å: Chain B: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.17 Hydrogen bonds: B:H.17, B:N.18, B:G.44, B:G.46, B:L.67, B:S.68, B:D.94, B:A.95 Water bridges: B:S.45, B:S.47, B:E.49, B:V.110 SAH.5: 19 residues within 4Å: Chain C: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:H.17 Hydrogen bonds: C:H.17, C:N.18, C:G.44, C:G.46, C:L.67, C:S.68, C:D.94, C:A.95 Water bridges: C:S.45, C:S.47, C:E.49, C:V.110 SAH.7: 19 residues within 4Å: Chain D: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:H.17 Hydrogen bonds: D:H.17, D:N.18, D:G.44, D:G.46, D:L.67, D:S.68, D:D.94, D:D.94, D:A.95 Water bridges: D:S.45, D:S.47, D:E.49, D:V.110 SAH.9: 19 residues within 4Å: Chain E: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:H.17 Hydrogen bonds: E:H.17, E:N.18, E:G.44, E:G.46, E:L.67, E:S.68, E:D.94, E:D.94, E:A.95 Water bridges: E:S.45, E:S.47, E:E.49, E:V.110 SAH.11: 19 residues within 4Å: Chain F: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:H.17 Hydrogen bonds: F:H.17, F:N.18, F:G.44, F:G.46, F:L.67, F:S.68, F:D.94, F:D.94, F:A.95 Water bridges: F:S.45, F:S.47, F:E.49, F:V.110 SAH.13: 19 residues within 4Å: Chain G: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:H.17 Hydrogen bonds: G:H.17, G:N.18, G:G.44, G:G.46, G:L.67, G:S.68, G:D.94, G:D.94, G:A.95 Water bridges: G:S.45, G:S.47, G:E.49, G:V.110 SAH.15: 19 residues within 4Å: Chain H: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:H.17 Hydrogen bonds: H:H.17, H:N.18, H:G.44, H:G.46, H:L.67, H:S.68, H:D.94, H:D.94, H:A.95 Water bridges: H:S.45, H:S.47, H:E.49, H:V.110 SAH.17: 19 residues within 4Å: Chain I: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:H.17 Hydrogen bonds: I:H.17, I:N.18, I:G.44, I:G.46, I:L.67, I:S.68, I:D.94, I:D.94, I:A.95 Water bridges: I:S.45, I:S.47, I:E.49, I:V.110 SAH.19: 19 residues within 4Å: Chain J: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:H.17 Hydrogen bonds: J:H.17, J:N.18, J:G.44, J:G.46, J:L.67, J:S.68, J:D.94, J:A.95 Water bridges: J:S.45, J:S.47, J:E.49, J:V.110 SAH.21: 19 residues within 4Å: Chain K: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 13 PLIP interactions: 13 interactions with chain K Hydrophobic interactions: K:H.17 Hydrogen bonds: K:H.17, K:N.18, K:G.44, K:G.46, K:L.67, K:S.68, K:D.94, K:A.95 Water bridges: K:S.45, K:S.47, K:E.49, K:V.110 SAH.23: 19 residues within 4Å: Chain L: I.3, I.16, H.17, N.18, G.44, S.45, G.46, D.66, L.67, S.68, F.71, G.93, D.94, A.95, V.110, G.111, A.112, W.114, I.115 13 PLIP interactions: 13 interactions with chain L Hydrophobic interactions: L:H.17 Hydrogen bonds: L:H.17, L:N.18, L:G.44, L:G.46, L:L.67, L:S.68, L:D.94, L:A.95 Water bridges: L:S.45, L:S.47, L:E.49, L:V.110

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

NA.2: 5 residues within 4Å: Chain A: D.188 Chain H: D.188, D.190 Ligands: NA.12, NA.16 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.190 NA.4: 5 residues within 4Å: Chain B: D.188 Chain L: D.188, D.190 Ligands: NA.14, NA.24 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:D.190 NA.6: 5 residues within 4Å: Chain C: D.188 Chain D: D.188, D.190 Ligands: NA.8, NA.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.190, D:D.190 NA.8: 5 residues within 4Å: Chain D: D.188 Chain K: D.188, D.190 Ligands: NA.6, NA.22 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain K Hydrogen bonds: D:D.188, K:D.190, K:D.190 NA.10: 5 residues within 4Å: Chain E: D.188 Chain I: D.188, D.190 Ligands: NA.18, NA.20 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain I Hydrogen bonds: E:D.188, E:D.188, I:D.190 NA.12: 5 residues within 4Å: Chain A: D.188, D.190 Chain F: D.188 Ligands: NA.2, NA.16 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:D.188, F:D.188 NA.14: 5 residues within 4Å: Chain B: D.188, D.190 Chain G: D.188 Ligands: NA.4, NA.24 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain G Hydrogen bonds: B:D.190, G:D.188, G:D.188 NA.16: 5 residues within 4Å: Chain F: D.188, D.190 Chain H: D.188 Ligands: NA.2, NA.12 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain F Hydrogen bonds: H:D.188, F:D.190, F:D.190 NA.18: 5 residues within 4Å: Chain I: D.188 Chain J: D.188, D.190 Ligands: NA.10, NA.20 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.188, I:D.188 NA.20: 5 residues within 4Å: Chain E: D.188, D.190 Chain J: D.188 Ligands: NA.10, NA.18 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:D.188 NA.22: 5 residues within 4Å: Chain C: D.188, D.190 Chain K: D.188 Ligands: NA.6, NA.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.188 NA.24: 5 residues within 4Å: Chain G: D.188, D.190 Chain L: D.188 Ligands: NA.4, NA.14 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.188, G:D.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

LaRowe, C. et al., Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine. to be published

Release Date

2015-11-25

Peptides

SAM-dependent methyltransferase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

SAM-dependent methyltransferase