SMTL ID : 5cxb.1

Structure of Ytm1 bound to the C-terminal domain of Erb1 in P21 21 2 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: K.200, D.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.200, A:D.248 Water bridges: A:D.248 EDO.2: 6 residues within 4Å: Chain A: D.83, S.117, L.118, D.436, R.438, V.457 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.83, A:L.118, A:D.436 EDO.3: 4 residues within 4Å: Chain A: I.60, R.61, Y.63, G.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.64

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: G.430, E.461, R.462, W.465, R.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.461, A:R.462, A:R.473

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: T.77, S.79, I.80 No protein-ligand interaction detected (PLIP) GOL.7: 6 residues within 4Å: Chain B: H.165, R.166, R.167, L.212, R.213, P.214 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.166, B:R.167, B:R.167, B:L.212

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

CL.6: 2 residues within 4Å: Chain B: G.53, Q.55 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wegrecki, M. et al., The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two beta-propellers during the assembly of large ribosomal subunits in eukaryotes. Nucleic Acids Res. (2015)

Release Date

2015-11-04

Peptides

Ribosome biogenesis protein YTM1: A
Ribosome biogenesis protein ERB1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosome biogenesis protein YTM1

Ribosome biogenesis protein ERB1

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