SMTL ID : 1wzn.1

Crystal Structure of the SAM-dependent methyltransferase from Pyrococcus horikoshii OT3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.77, R.81 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.77, A:R.81 SO4.4: 2 residues within 4Å: Chain B: R.77, R.81 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.77 Salt bridges: B:R.77, B:R.81 SO4.6: 2 residues within 4Å: Chain C: R.77, R.81 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.77, C:R.81 Salt bridges: C:R.77, C:R.81 SO4.8: 2 residues within 4Å: Chain D: R.77, R.81 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.77, D:R.81 SO4.11: 2 residues within 4Å: Chain E: R.77, R.81 3 PLIP interactions: 3 interactions with chain E Water bridges: E:R.77 Salt bridges: E:R.77, E:R.81 SO4.13: 2 residues within 4Å: Chain F: R.77, R.81 4 PLIP interactions: 4 interactions with chain F Water bridges: F:R.77, F:R.81 Salt bridges: F:R.77, F:R.81

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.120 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, H2O.3, H2O.7 MG.9: 1 residues within 4Å: Chain D: D.120 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.120, H2O.26, H2O.31

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

SAH.3: 19 residues within 4Å: Chain A: Y.5, Y.12, R.19, A.49, C.50, G.51, I.54, P.55, D.70, L.71, H.72, M.75, G.95, D.96, V.97, F.112, F.113, T.115, F.119 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.12, A:G.51, A:L.71, A:H.72, A:H.72, A:D.96, A:D.96, A:V.97, A:F.112, A:T.115 Water bridges: A:F.112, A:F.112 Salt bridges: A:R.19 SAH.5: 19 residues within 4Å: Chain B: Y.5, Y.12, R.19, A.49, C.50, G.51, I.54, P.55, D.70, L.71, H.72, M.75, G.95, D.96, V.97, F.112, F.113, T.115, F.119 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.12, B:L.71, B:H.72, B:H.72, B:D.96, B:D.96, B:V.97, B:F.112, B:T.115 Water bridges: B:I.54, B:F.112, B:F.112 Salt bridges: B:R.19 SAH.7: 18 residues within 4Å: Chain C: Y.5, Y.12, R.19, A.49, C.50, G.51, P.55, D.70, L.71, H.72, M.75, G.95, D.96, V.97, F.112, F.113, T.115, F.119 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.12, C:Y.12, C:L.71, C:H.72, C:H.72, C:D.96, C:V.97, C:F.112, C:T.115 Water bridges: C:Y.2, C:I.54, C:F.112 Salt bridges: C:R.19 SAH.10: 19 residues within 4Å: Chain D: Y.5, Y.12, R.19, A.49, C.50, G.51, I.54, P.55, D.70, L.71, H.72, M.75, G.95, D.96, V.97, F.112, F.113, T.115, F.119 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.12, D:Y.12, D:G.51, D:L.71, D:H.72, D:H.72, D:D.96, D:V.97, D:F.112 Water bridges: D:Y.2, D:F.112, D:F.112 Salt bridges: D:R.19 SAH.12: 19 residues within 4Å: Chain E: Y.5, Y.12, R.19, A.49, C.50, G.51, I.54, P.55, D.70, L.71, H.72, M.75, G.95, D.96, V.97, F.112, F.113, T.115, F.119 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:Y.12, E:Y.12, E:L.71, E:H.72, E:H.72, E:D.96, E:V.97, E:F.112 Water bridges: E:Y.2, E:I.54, E:F.112, E:F.112 Salt bridges: E:R.19 SAH.14: 18 residues within 4Å: Chain F: Y.5, Y.12, R.19, A.49, C.50, G.51, P.55, D.70, L.71, H.72, M.75, G.95, D.96, V.97, F.112, F.113, T.115, F.119 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:Y.12, F:L.71, F:H.72, F:H.72, F:D.96, F:D.96, F:V.97, F:F.112 Water bridges: F:I.54, F:F.112 Salt bridges: F:R.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizutani, H. et al., Crystal Structure of the SAM-dependent methyltransferase from Pyrococcus horikoshii OT3. To be Published

Release Date

2006-03-14

Peptides

SAM-dependent methyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

SAM-dependent methyltransferase