SMTL ID : 5k8v.1

Crystal Structure of Mus musculus Protein Arginine Methyltransferase 4 (CARM1 130-487) with CP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x 6RE: [[2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethylamino]-azanyl-methylidene]azanium(Non-covalent)

6RE.1: 25 residues within 4Å: Chain A: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, E.141, M.143, S.146, W.290 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Y.28, A:Q.34, A:G.67, A:G.69, A:E.89, A:E.89, A:A.90, A:S.91, A:V.117, A:E.118, A:M.134, A:M.134 Water bridges: A:R.15, A:W.290, A:W.290 Salt bridges: A:E.132, A:E.141 pi-Stacking: A:F.25 6RE.8: 25 residues within 4Å: Chain B: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, E.141, M.143, S.146, W.290 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Y.28, B:G.67, B:G.69, B:E.89, B:E.89, B:A.90, B:S.91, B:V.117, B:E.118, B:M.134, B:M.134 Water bridges: B:R.15, B:Q.34, B:W.290, B:W.290 Salt bridges: B:E.132, B:E.141 pi-Stacking: B:F.25 6RE.12: 24 residues within 4Å: Chain C: F.12, Y.24, F.25, Y.28, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, E.141, M.143, S.146, W.290 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.28 Hydrogen bonds: C:Y.28, C:Q.34, C:G.67, C:E.89, C:A.90, C:S.91, C:S.91, C:S.91, C:V.117, C:E.118, C:M.134, C:M.134 Water bridges: C:R.15, C:W.290, C:W.290 Salt bridges: C:E.132, C:E.141 pi-Stacking: C:F.25 6RE.16: 25 residues within 4Å: Chain D: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, E.141, M.143, S.146, W.290 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:Y.28, D:Q.34, D:G.67, D:G.69, D:E.89, D:E.89, D:A.90, D:S.91, D:V.117, D:E.118, D:M.134, D:M.134 Water bridges: D:R.15, D:W.290, D:W.290 Salt bridges: D:E.132, D:E.141 pi-Stacking: D:F.25

1 x DXE: 1,2-DIMETHOXYETHANE(Non-covalent)

DXE.2: 7 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, N.140, E.141, K.345 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain A: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: F.27, Y.30, S.32, Q.33 Chain B: N.346 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.32 Water bridges: B:N.346 EDO.5: 6 residues within 4Å: Chain A: L.52, Q.53 Chain D: D.332, Q.333, T.334, G.335 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: D.57, N.159, I.271, G.272, S.273 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.159, A:N.159 EDO.10: 6 residues within 4Å: Chain B: Y.24, F.27, Y.28, N.140, E.141, K.345 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.140 EDO.13: 6 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, E.141, K.345 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain C: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.15: 6 residues within 4Å: Chain C: K.151, L.154, K.155, P.156, G.158, L.235 1 PLIP interactions: 1 interactions with chain C Water bridges: C:P.156 EDO.17: 7 residues within 4Å: Chain D: Q.23, Y.24, F.27, Y.28, N.140, E.141, K.345 No protein-ligand interaction detected (PLIP) EDO.18: 3 residues within 4Å: Chain D: D.267, W.278, S.280 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.267

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: T.173, D.219, R.221, I.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.219 PEG.11: 3 residues within 4Å: Chain B: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP)

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.9: 11 residues within 4Å: Chain B: R.9, S.10, P.114, G.115, K.116, E.118, E.119, V.120, S.121, K.152, Y.153 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.122, B:K.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cura, V. et al., Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors. FEBS J. (2017)

Release Date

2016-11-09

Peptides

Histone-arginine methyltransferase CARM1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Histone-arginine methyltransferase CARM1

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