SMTL ID : 5lkj.1

Crystal structure of mouse CARM1 in complex with ligand SA684

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x 6YB: (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-carbamimidamidoethyl)amino]-2-azanyl-butanoic acid(Non-covalent)

6YB.1: 31 residues within 4Å: Chain A: F.12, Y.24, F.25, Y.28, Q.34, M.37, M.38, R.43, G.67, C.68, G.69, S.70, I.72, L.73, 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, H.289, W.290 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Y.28, A:Q.34, A:Q.34, A:G.67, A:E.89, A:E.89, A:A.90, A:V.117, A:S.146, A:H.289, A:H.289, A:W.290 Water bridges: A:R.15, A:L.73 Salt bridges: A:R.43, A:E.132, A:E.132, A:E.141 pi-Stacking: A:F.25 6YB.10: 32 residues within 4Å: Chain B: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, R.43, G.67, C.68, G.69, S.70, G.71, I.72, L.73, 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, H.289, W.290 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Y.28, B:Q.34, B:Q.34, B:G.67, B:E.89, B:E.89, B:A.90, B:V.117, B:E.118, B:H.289, B:H.289, B:W.290 Water bridges: B:R.15 Salt bridges: B:R.43, B:E.132, B:E.132, B:E.141 pi-Stacking: B:F.25 6YB.17: 30 residues within 4Å: Chain C: F.12, Y.24, F.25, Y.28, Q.34, M.37, R.43, D.65, G.67, C.68, G.69, S.70, G.71, I.72, L.73, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, M.134, G.135, E.141, M.143, S.146, W.290 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:Y.28, C:Q.34, C:Q.34, C:G.67, C:E.89, C:E.89, C:A.90, C:S.91, C:S.91, C:V.117, C:E.118, C:E.132, C:M.134, C:W.290 Salt bridges: C:R.43, C:E.132, C:E.132, C:E.141 pi-Stacking: C:F.25 6YB.21: 32 residues within 4Å: Chain D: F.12, Y.24, F.25, Y.28, Q.34, M.37, R.43, D.65, G.67, C.68, G.69, S.70, G.71, I.72, L.73, 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, H.289, W.290 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Y.28, D:Y.28, D:Q.34, D:C.68, D:E.89, D:E.89, D:A.90, D:S.91, D:V.117, D:S.146, D:H.289, D:W.290 Salt bridges: D:R.43, D:E.132, D:E.132, D:E.141 pi-Stacking: D:F.25

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

EDO.2: 7 residues within 4Å: Chain A: Q.48, L.52, Q.79 Chain D: D.332, Q.333, T.334, G.335 No protein-ligand interaction detected (PLIP) EDO.3: 6 residues within 4Å: Chain A: P.248, F.249, K.250, S.310, G.311, T.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.249 EDO.4: 2 residues within 4Å: Chain A: Y.230, T.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.231, A:T.231 EDO.5: 4 residues within 4Å: Chain A: K.151, L.154, K.155, P.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.154, A:L.235 EDO.11: 6 residues within 4Å: Chain B: D.40, L.287, T.288, H.289, Y.291, Y.351 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.291 EDO.12: 6 residues within 4Å: Chain B: K.151, L.154, K.155, P.156, G.158, L.235 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.156 EDO.13: 5 residues within 4Å: Chain A: T.183, K.184, F.187 Chain B: Q.35, Q.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.35, B:Q.39 EDO.18: 2 residues within 4Å: Chain C: D.267, W.278 No protein-ligand interaction detected (PLIP)

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

DXE.6: 8 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, Y.136, N.140, E.141, K.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.28 DXE.7: 7 residues within 4Å: Chain A: N.36, D.40, L.287, T.288, H.289, Y.291, Y.351 No protein-ligand interaction detected (PLIP) DXE.8: 4 residues within 4Å: Chain A: D.267, W.278, S.280, E.285 No protein-ligand interaction detected (PLIP) DXE.15: 7 residues within 4Å: Chain A: Q.23, Q.26, F.27, Y.30, Q.33 Chain B: Q.23, N.346 No protein-ligand interaction detected (PLIP) DXE.16: 9 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, Y.136, N.140, E.141, K.345, F.349 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.28

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

PEG.9: 8 residues within 4Å: Chain A: D.57, S.157, G.158, N.159, L.235, I.271, G.272, S.273 No protein-ligand interaction detected (PLIP) PEG.19: 8 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, Y.136, N.140, E.141, K.345 No protein-ligand interaction detected (PLIP) PEG.20: 6 residues within 4Å: Chain C: N.36, D.40, L.287, T.288, H.289, Y.291 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.291, C:Y.291

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.14: 8 residues within 4Å: Chain B: S.10, E.118, E.119, V.120, S.121, Q.125, K.152, Y.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.125 Water bridges: B:Y.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cura, V. et al., Crystal structure of mouse CARM1 in complex with ligands. To Be Published

Release Date

2017-08-16

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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