SMTL ID : 7uui.1

Nucleoplasmic pre-60S intermediate of the Nog2 containing post-rotation state from a SPB1 D52A strain

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.329, Q.342, T.350, D.366 Ligands: GDP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.329, A:T.350

1 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: N.325, A.344, I.346, E.349 Ligands: GDP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.344

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 17 residues within 4Å: Chain A: N.260, K.261, D.263, L.264, H.287, A.288, N.325, T.326, G.327, K.328, S.329, S.330, V.343, A.344, P.345 Ligands: MG.1, K.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.260, A:K.261, A:K.261, A:A.288, A:N.325, A:T.326, A:G.327, A:K.328, A:S.329, A:S.330, A:S.330, A:A.344 Salt bridges: A:D.263, A:K.328 pi-Cation interactions: A:K.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sekulski, K. et al., rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly. Nat Commun (2023)

Release Date

2023-03-15

Peptides

Nucleolar GTP-binding protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
m

Nucleolar GTP-binding protein 2

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