SMTL ID : 9jgb.1

Crystal structure of Nep1 from Pyrococcus horikoshii OT3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.4, K.5, R.86, K.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.5 Salt bridges: A:R.86, A:K.225 SO4.5: 4 residues within 4Å: Chain B: K.4, K.5, R.86, K.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.5 Salt bridges: B:R.86, B:K.225

2 x SO3: SULFITE ION(Non-covalent)

SO3.2: 6 residues within 4Å: Chain A: R.106, P.108, R.109, N.110, R.113 Chain B: R.65 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.106, A:R.106, A:R.109, A:N.110, A:R.113 SO3.6: 6 residues within 4Å: Chain A: R.65 Chain B: R.106, P.108, R.109, N.110, R.113 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.106, B:R.106, B:R.109, B:N.110, B:R.113

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: N.82, P.103, E.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.82, A:N.82 EDO.7: 3 residues within 4Å: Chain B: N.82, P.103, E.104 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.82, B:N.82

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: T.18, E.41, F.122 No protein-ligand interaction detected (PLIP) PEG.8: 3 residues within 4Å: Chain B: T.18, E.41, F.122 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saha, S. et al., Structural analysis of the ribosome assembly factor Nep1, an N1-specific pseudouridine methyltransferase, reveals mechanistic insights. Febs J. (2025)

Release Date

2025-03-12

Peptides

Ribosomal RNA small subunit methyltransferase Nep1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribosomal RNA small subunit methyltransferase Nep1

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