SMTL ID : 8x6l.1

PRMT5:MEP50 WITH SCR-6920 AND SAM

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 18 residues within 4Å: Chain A: L.315, L.319, Y.324, K.333, Y.334, G.365, P.370, L.371, E.392, K.393, N.394, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: YFU.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.324, A:G.365, A:G.365, A:K.393, A:N.394, A:M.420, A:R.421 Salt bridges: A:K.333, A:E.435 SAM.4: 18 residues within 4Å: Chain C: L.315, L.319, Y.324, K.333, Y.334, G.365, P.370, L.371, E.392, K.393, N.394, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: YFU.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.324, C:G.365, C:G.365, C:K.393, C:N.394, C:M.420, C:R.421 Salt bridges: C:K.333, C:E.435 SAM.7: 18 residues within 4Å: Chain E: L.315, L.319, Y.324, K.333, Y.334, G.365, P.370, L.371, E.392, K.393, N.394, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: YFU.9 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Y.324, E:Y.324, E:Y.334, E:G.365, E:K.393, E:N.394, E:D.419, E:M.420, E:R.421, E:E.435 Salt bridges: E:K.333, E:E.435 SAM.10: 18 residues within 4Å: Chain F: L.315, L.319, Y.324, K.333, Y.334, G.365, P.370, L.371, E.392, K.393, N.394, D.419, M.420, R.421, E.435, L.436, C.449 Ligands: YFU.12 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Y.324, F:Y.324, F:Y.334, F:G.365, F:G.365, F:K.393, F:N.394, F:D.419, F:M.420, F:R.421, F:E.435 Salt bridges: F:K.333, F:E.435

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: T.80, V.83, P.120, W.152, Q.263 No protein-ligand interaction detected (PLIP) GOL.5: 5 residues within 4Å: Chain C: T.80, V.83, P.120, W.152, Q.263 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain E: T.80, V.83, P.120, W.152, Q.263 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain F: T.80, V.83, P.120, W.152, Q.263 No protein-ligand interaction detected (PLIP)

4 x YFU: 1-ethyl-8-[(2-methoxy-7-azaspiro[3.5]nonan-7-yl)carbonyl]-4-[2-oxidanylidene-2-[(3~{S})-1,2,3,4-tetrahydroisoquinolin-3-yl]ethyl]-2,3-dihydro-1,4-benzodiazepin-5-one(Non-covalent)

YFU.3: 17 residues within 4Å: Chain A: F.300, Y.304, Q.309, L.312, L.319, V.326, F.327, K.333, G.438, S.439, E.444, V.503, F.577, S.578, W.579, F.580 Ligands: SAM.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.300, A:Y.304, A:Q.309, A:L.312, A:L.319, A:V.326, A:F.327, A:F.577, A:F.577, A:F.580, A:F.580, A:F.580 Hydrogen bonds: A:S.439, A:W.579, A:F.580 pi-Stacking: A:F.327, A:F.327 YFU.6: 17 residues within 4Å: Chain C: F.300, Y.304, Q.309, L.312, L.319, V.326, F.327, K.333, G.438, S.439, E.444, V.503, F.577, S.578, W.579, F.580 Ligands: SAM.4 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.300, C:Y.304, C:Q.309, C:L.312, C:L.319, C:V.326, C:F.327, C:F.577, C:F.577, C:F.580, C:F.580, C:F.580 Hydrogen bonds: C:S.439, C:W.579, C:F.580 pi-Stacking: C:F.327, C:F.327 YFU.9: 17 residues within 4Å: Chain E: F.300, Y.304, Q.309, L.312, L.319, V.326, F.327, K.333, G.438, S.439, E.444, V.503, F.577, S.578, W.579, F.580 Ligands: SAM.7 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:F.300, E:Y.304, E:Q.309, E:L.312, E:L.319, E:V.326, E:F.327, E:F.577, E:F.577, E:F.580, E:F.580, E:F.580 Hydrogen bonds: E:S.439, E:W.579, E:F.580 pi-Stacking: E:F.327, E:F.327 YFU.12: 17 residues within 4Å: Chain F: F.300, Y.304, Q.309, L.312, L.319, V.326, F.327, K.333, G.438, S.439, E.444, V.503, F.577, S.578, W.579, F.580 Ligands: SAM.10 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:F.300, F:Y.304, F:Q.309, F:L.312, F:L.319, F:V.326, F:F.327, F:F.577, F:F.577, F:F.580, F:F.580, F:F.580 Hydrogen bonds: F:S.439, F:W.579, F:F.580 pi-Stacking: F:F.327, F:F.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, F. et al., PRMT5:MEP50 WITH SCR-6920 AND SAM. To Be Published

Release Date

2025-02-26

Peptides

Protein arginine N-methyltransferase 5: ACEF
Methylosome protein WDR77: BDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

F
F

B
B

D
D

G
G

H
H

Protein arginine N-methyltransferase 5

Methylosome protein WDR77

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