SMTL ID : 3o7b.1

Crystal structure of Archaeoglobus Fulgidus Nep1 bound to S-adenosylhomocysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x TYR: TYROSINE(Non-covalent)

TYR.1: 6 residues within 4Å: Chain A: R.178, S.216, L.217, G.218, T.219, R.230 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:R.178, A:T.219 Hydrogen bonds: A:L.217, A:R.230 Water bridges: A:S.216 Salt bridges: A:R.178 TYR.3: 6 residues within 4Å: Chain B: R.178, S.216, L.217, G.218, T.219, R.230 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:R.178, B:T.219 Hydrogen bonds: B:L.217, B:R.230 Water bridges: B:S.216 Salt bridges: B:R.178

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

SAH.2: 18 residues within 4Å: Chain A: F.172, R.173, E.174, I.193, G.194, F.196, P.197, G.199, F.201, V.215, S.216, L.217, G.218, E.220, S.221, Y.222, S.224, V.227 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.196 Hydrogen bonds: A:G.194, A:G.199, A:L.217, A:G.218, A:E.220, A:S.221, A:Y.222 Water bridges: A:E.174, A:G.194 SAH.4: 18 residues within 4Å: Chain B: F.172, R.173, E.174, I.193, G.194, F.196, P.197, G.199, F.201, V.215, S.216, L.217, G.218, E.220, S.221, Y.222, S.224, V.227 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.196 Hydrogen bonds: B:G.194, B:G.199, B:L.217, B:G.218, B:E.220, B:S.221, B:Y.222 Water bridges: B:E.174, B:E.174, B:G.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, S.R. et al., Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Nucleic Acids Res. (2011)

Release Date

2011-01-19

Peptides

Ribosome biogenesis Nep1 RNA methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribosome biogenesis Nep1 RNA methyltransferase