SMTL ID : 8sig.1

Crystal Structure of PRMT4 with Compound YD1-288

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x GWU: 5'-{(3-aminopropyl)[2-(benzylcarbamamido)ethyl]amino}-5'-deoxyadenosine

GWU.1: 24 residues within 4Å: Chain A: Y.28, F.29, Y.32, Q.38, R.47, T.48, Y.51, G.71, C.72, G.73, I.76, L.77, E.93, A.94, S.95, G.119, K.120, V.121, E.122, E.136, M.138, E.145, M.147, S.150 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:R.47, A:Y.51, A:I.76, A:L.77, A:L.77, A:E.136 Hydrogen bonds: A:Y.28, A:Q.38, A:R.47, A:R.47, A:G.71, A:G.73, A:A.94, A:S.95, A:V.121, A:E.122, A:M.138, A:S.150 Water bridges: A:D.69, A:L.77, A:E.136, A:E.136 Salt bridges: A:E.145 pi-Stacking: A:F.29 pi-Cation interactions: A:R.47 GWU.10: 24 residues within 4Å: Chain B: Y.28, F.29, Y.32, Q.38, R.47, T.48, Y.51, G.71, C.72, G.73, I.76, L.77, E.93, A.94, S.95, G.119, K.120, V.121, E.122, E.136, M.138, E.145, M.147, S.150 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:R.47, B:Y.51, B:I.76, B:L.77, B:L.77, B:E.136 Hydrogen bonds: B:Q.38, B:R.47, B:R.47, B:G.71, B:G.73, B:A.94, B:S.95, B:V.121, B:E.122, B:M.138, B:S.150 Water bridges: B:D.69, B:L.77, B:E.136, B:E.136 Salt bridges: B:E.145 pi-Stacking: B:F.29 pi-Cation interactions: B:R.47

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

NA.2: 1 residues within 4Å: Chain A: E.179 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.178, A:D.178, A:R.225 NA.11: 1 residues within 4Å: Chain B: E.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.179 Water bridges: B:E.179, B:R.225

14 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 2 residues within 4Å: Chain A: F.214, Q.302 No protein-ligand interaction detected (PLIP) UNX.4: 2 residues within 4Å: Chain B: S.196, H.198 No protein-ligand interaction detected (PLIP) UNX.5: 1 residues within 4Å: Chain A: W.294 No protein-ligand interaction detected (PLIP) UNX.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: D.245, R.248 No protein-ligand interaction detected (PLIP) UNX.8: 1 residues within 4Å: Chain A: G.276 No protein-ligand interaction detected (PLIP) UNX.9: 2 residues within 4Å: Chain A: E.149, A.321 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain B: F.214, Q.302 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain A: S.196, H.198 No protein-ligand interaction detected (PLIP) UNX.14: 1 residues within 4Å: Chain B: W.294 No protein-ligand interaction detected (PLIP) UNX.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.16: 2 residues within 4Å: Chain B: D.245, R.248 No protein-ligand interaction detected (PLIP) UNX.17: 1 residues within 4Å: Chain B: G.276 No protein-ligand interaction detected (PLIP) UNX.18: 2 residues within 4Å: Chain B: E.149, A.321 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, X. et al., Crystal Structure of PRMT4 with Compound YD1-288. To be published

Release Date

2024-04-24

Peptides

Histone-arginine methyltransferase CARM1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone-arginine methyltransferase CARM1

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