SMTL ID : 8sih.1

Crystal Structure of PRMT4 with Compound YD1-289

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x I1K: 5'-{[2-(benzylcarbamamido)ethyl][3-(N'-cyclopentylcarbamimidamido)propyl]amino}-5'-deoxyadenosine

I1K.1: 28 residues within 4Å: Chain A: Y.28, F.29, Y.32, Q.38, M.41, D.44, 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, H.293, W.294 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:R.47, A:I.76, A:L.77, A:L.77, A:E.136, A:E.136, A:H.293, A:W.294, A:W.294, A:W.294 Hydrogen bonds: A:Y.32, A:Y.32, A:Q.38, A:R.47, A:G.71, A:G.71, A:C.72, A:G.73, A:A.94, A:S.95, A:V.121, A:E.122, A:M.138, A:S.150 Water bridges: A:L.77 Salt bridges: A:E.136, A:E.136, A:E.145 pi-Stacking: A:F.29, A:Y.51 pi-Cation interactions: A:R.47 I1K.4: 28 residues within 4Å: Chain B: Y.28, F.29, Y.32, Q.38, M.41, D.44, 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, H.293, W.294 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:R.47, B:I.76, B:L.77, B:L.77, B:E.136, B:E.136, B:H.293, B:W.294, B:W.294, B:W.294 Hydrogen bonds: B:Y.32, B:Q.38, B:R.47, B:G.71, B:G.71, B:C.72, B:G.73, B:A.94, B:S.95, B:V.121, B:E.122, B:M.138, B:S.150 Water bridges: B:L.77 Salt bridges: B:E.136, B:E.136, B:E.145 pi-Stacking: B:F.29, B:Y.51 pi-Cation interactions: B:R.47

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: F.79, Q.83 Chain B: G.199 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: S.196, H.198 No protein-ligand interaction detected (PLIP) CA.5: 3 residues within 4Å: Chain A: G.199 Chain B: F.79, Q.83 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain B: S.196, H.198 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 YD1-289. 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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