SMTL ID : 3oin.1

Crystal structure of Saccharomyces cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 1 residues within 4Å: Chain A: K.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.40 GOL.2: 2 residues within 4Å: Chain A: V.163, K.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.165

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

SAH.3: 21 residues within 4Å: Chain B: L.181, S.182, F.183, V.207, G.208, M.210, A.211, R.212, G.213, D.215, F.217, G.227, L.228, S.229, Y.231, P.232, L.233, S.234, A.235, A.238 Chain C: U.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.208, B:G.208, B:G.213, B:D.215, B:L.228, B:S.229, B:S.229, B:L.233 Water bridges: B:F.183

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 2 residues within 4Å: Chain C: G.3, C.4 No protein-ligand interaction detected (PLIP)

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

CL.5: 3 residues within 4Å: Chain C: G.3, C.4, C.13 Ligand excluded by PLIP

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

2010-12-01

Peptides

Ribosomal RNA small subunit methyltransferase NEP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosomal RNA small subunit methyltransferase NEP1

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