SMTL ID : 6v0o.2 (1 other biounit)

PRMT5 bound to the PBM peptide from pICln

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 25 residues within 4Å: Chain A: P.314, L.315, L.319, Y.324, F.327, E.328, K.333, Y.334, G.365, A.366, G.367, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, E.444, C.449 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:P.314, A:Y.324, A:Y.324, A:Y.334, A:G.365, A:G.367, A:K.393, A:D.419, A:M.420, A:E.435 Salt bridges: A:K.333 pi-Cation interactions: A:K.393 SFG.3: 25 residues within 4Å: Chain D: P.314, L.315, L.319, Y.324, F.327, E.328, K.333, Y.334, G.365, A.366, G.367, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, E.444, C.449 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:P.314, D:Y.324, D:Y.324, D:Y.334, D:G.365, D:G.367, D:K.393, D:D.419, D:M.420, D:E.435 Salt bridges: D:K.333 pi-Cation interactions: D:K.393 SFG.5: 25 residues within 4Å: Chain G: P.314, L.315, L.319, Y.324, F.327, E.328, K.333, Y.334, G.365, A.366, G.367, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, E.444, C.449 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:P.314, G:Y.324, G:Y.334, G:Y.334, G:G.365, G:G.367, G:K.393, G:D.419, G:M.420, G:E.435 Salt bridges: G:K.333 pi-Cation interactions: G:K.393 SFG.7: 25 residues within 4Å: Chain J: P.314, L.315, L.319, Y.324, F.327, E.328, K.333, Y.334, G.365, A.366, G.367, P.370, L.371, V.391, E.392, K.393, N.394, S.418, D.419, M.420, R.421, E.435, L.436, E.444, C.449 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:P.314, J:Y.324, J:Y.334, J:Y.334, J:G.365, J:G.367, J:K.393, J:D.419, J:M.420, J:E.435 Salt bridges: J:K.333 pi-Cation interactions: J:K.393

4 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.2: 2 residues within 4Å: Chain A: Y.304, Q.309 No protein-ligand interaction detected (PLIP) ACE.4: 2 residues within 4Å: Chain D: Y.304, Q.309 No protein-ligand interaction detected (PLIP) ACE.6: 2 residues within 4Å: Chain G: Y.304, Q.309 No protein-ligand interaction detected (PLIP) ACE.8: 2 residues within 4Å: Chain J: Y.304, Q.309 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mulvaney, K.M. et al., Molecular basis for substrate recruitment to the PRMT5 methylosome. Mol.Cell (2021)

Release Date

2020-08-26

Peptides

Protein arginine N-methyltransferase 5: ADGJ
Methylosome protein 50: BEHK
PBM peptide: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
D

F
D

I
D

L
D

Protein arginine N-methyltransferase 5

Methylosome protein 50

PBM peptide

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