SMTL ID : 7qrd.1

Crystal structure of mouse CARM1 in complex with histone H3_10-25

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-4-2-mer

Ligands

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

EDO.1: 9 residues within 4Å: Chain B: Y.25, M.34, E.129, M.131, G.132, E.138, H.286, W.287 Ligands: SAH.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.129, B:E.138 EDO.2: 8 residues within 4Å: Chain B: Y.133, N.137, K.342, N.343, P.344, F.346 Chain F: K.5 Ligands: MLI.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.137 EDO.5: 8 residues within 4Å: Chain D: F.24, Y.133, N.137, K.342, P.344, F.346 Chain E: K.5 Ligands: MLI.8 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.133, D:N.137, D:K.342 EDO.6: 11 residues within 4Å: Chain D: Y.25, M.34, R.40, E.129, P.130, M.131, G.132, E.138, H.286, W.287 Ligands: SAH.7 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.129, D:H.286

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 5 residues within 4Å: Chain B: Q.20, F.24, K.342 Chain F: K.5 Ligands: EDO.2 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Water bridges: F:S.1 Salt bridges: F:K.5, F:K.5, B:K.342 MLI.8: 6 residues within 4Å: Chain D: Q.20, F.24, K.342 Chain E: S.1, K.5 Ligands: EDO.5 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:Q.20, E:K.5 Salt bridges: D:K.342, E:K.5 Hydrogen bonds: E:S.1

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 29 residues within 4Å: Chain B: F.9, Y.21, F.22, Y.25, Q.31, M.34, M.35, R.40, D.62, G.64, C.65, G.66, S.67, G.68, I.69, L.70, V.85, E.86, A.87, S.88, G.112, K.113, V.114, E.115, E.129, P.130, M.140, S.143 Ligands: EDO.1 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.31, B:Q.31, B:G.64, B:G.64, B:E.86, B:E.86, B:A.87, B:S.88, B:V.114, B:E.115 Water bridges: B:R.12, B:G.68 Salt bridges: B:R.40 pi-Stacking: B:F.22 SAH.7: 26 residues within 4Å: Chain D: F.9, Y.21, F.22, Y.25, Q.31, M.34, M.35, R.40, G.64, C.65, G.66, S.67, I.69, L.70, V.85, E.86, A.87, S.88, G.112, K.113, V.114, E.115, E.129, M.140, S.143 Ligands: EDO.6 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.31, D:G.64, D:C.65, D:G.66, D:E.86, D:E.86, D:A.87, D:S.88, D:V.114, D:E.115 Water bridges: D:R.12, D:G.68, D:E.129 Salt bridges: D:R.40 pi-Stacking: D:F.22

2 x QVR: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol(Covalent)

QVR.9: 22 residues within 4Å: Chain C: F.9, Y.21, F.22, Y.25, Q.31, M.34, G.64, G.66, V.85, E.86, A.87, S.88, G.112, K.113, V.114, E.115, E.129, P.130, E.138, M.140, S.143 Chain E: R.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.64, C:G.64, C:G.66, C:E.86, C:A.87, C:S.88, C:V.114, C:E.115 Water bridges: C:R.12 pi-Stacking: C:F.22 QVR.10: 23 residues within 4Å: Chain A: F.9, Y.21, F.22, Y.25, Q.31, M.34, G.64, G.66, V.85, E.86, A.87, S.88, G.112, K.113, V.114, E.115, E.129, P.130, M.131, E.138, M.140, S.143 Chain F: R.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.25 Hydrogen bonds: A:Q.31, A:G.64, A:E.86, A:E.86, A:A.87, A:V.114, A:E.115 Water bridges: A:R.12 pi-Stacking: A:F.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marechal, N. et al., CARM1 Transition State Mimics. To Be Published

Release Date

2022-12-28

Peptides

Histone-arginine methyltransferase CARM1: ABCD
SER-THR-GLY-GLY-LYS-ALA-PRO-URU-LYS-GLN-LEU-ALA-THR-LYS-ALA-ALA: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
L

F
M

Histone-arginine methyltransferase CARM1

SER-THR-GLY-GLY-LYS-ALA-PRO-URU-LYS-GLN-LEU-ALA-THR-LYS-ALA-ALA