SMTL ID : 8pb3.1

PsiM in complex with SAH and norbaeocystin, monoclinic crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 25 residues within 4Å: Chain A: L.81, P.83, R.88, D.118, I.119, G.120, T.121, G.122, I.126, Y.127, T.143, E.144, V.145, E.146, T.171, S.172, I.173, I.177, N.196, P.197, P.198, I.228, E.229, F.239 Ligands: XP6.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.120, A:G.122, A:Y.127, A:E.144, A:E.144, A:V.145, A:S.172, A:N.196 Water bridges: A:T.143 Salt bridges: A:R.88 SAH.7: 25 residues within 4Å: Chain B: L.81, P.83, R.88, D.118, I.119, G.120, T.121, G.122, I.126, Y.127, T.143, E.144, V.145, E.146, T.171, S.172, I.173, I.177, N.196, P.197, P.198, I.228, E.229, F.239 Ligands: XP6.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.120, B:G.122, B:Y.127, B:E.144, B:E.144, B:V.145, B:T.171, B:N.196 Water bridges: B:T.143, B:T.171, B:S.172, B:T.232 Salt bridges: B:R.88

2 x XP6: Norbaeocystin(Non-covalent)

XP6.2: 15 residues within 4Å: Chain A: L.81, T.84, R.88, N.196, P.197, P.198, F.199, Y.200, A.212, F.215, G.216, H.223, M.230, R.294 Ligands: SAH.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.199, A:F.215, A:H.223 Hydrogen bonds: A:N.196, A:N.196, A:Y.200, A:Y.200, A:G.216 Water bridges: A:T.84, A:G.216, A:R.294, A:R.294, A:R.294 Salt bridges: A:R.88, A:R.294 pi-Stacking: A:F.215 XP6.8: 15 residues within 4Å: Chain B: L.81, T.84, R.88, N.196, P.197, P.198, F.199, Y.200, A.212, F.215, G.216, H.223, M.230, R.294 Ligands: SAH.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.199, B:F.215, B:H.223 Hydrogen bonds: B:N.196, B:P.197, B:Y.200, B:Y.200, B:G.216 Water bridges: B:T.84, B:R.294, B:R.294, B:R.294, B:R.294 Salt bridges: B:R.88, B:R.294 pi-Stacking: B:F.215

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: G.13, M.14, H.15, N.90, Y.287 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 2 residues within 4Å: Chain A: N.285, E.286 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: G.71, L.72 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.71, H2O.5, H2O.11 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain A: E.183 Chain B: I.177, Q.242 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.183, H2O.15, H2O.17, H2O.23, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hudspeth, J. et al., Methyl transfer in psilocybin biosynthesis. Nat Commun (2024)

Release Date

2024-04-03

Peptides

Psilocybin synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Psilocybin synthase

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