SMTL ID : 5isf.1

Crystal structure of mouse CARM1 in complex with inhibitor SA0705

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-tetramer

Ligands

3 x 6D4: 5'-{[(3S)-3-amino-3-carboxypropyl][2-(triazan-1-yl)ethyl]amino}-5'-deoxyadenosine(Non-covalent)

6D4.1: 33 residues within 4Å: Chain A: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, M.38, 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, E.141, M.143, S.146, H.289, W.290 Ligands: PG4.4 17 PLIP interactions: 17 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:S.91, A:V.117, A:E.118, A:E.132, A:H.289 Water bridges: A:R.15, A:G.71 Salt bridges: A:R.43, A:E.132 pi-Stacking: A:F.25 6D4.8: 31 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, 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, E.141, M.143, S.146, H.289, W.290 Ligands: PG4.13 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:Q.34, B:G.67, B:S.70, B:E.89, B:E.89, B:A.90, B:V.117, B:E.118, B:E.132, B:E.132, B:M.134, B:M.134, B:W.290 Water bridges: B:R.15, B:G.71, B:L.73, B:E.132 Salt bridges: B:R.43, B:E.132 pi-Stacking: B:F.25 6D4.19: 31 residues within 4Å: Chain D: 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, E.141, M.143, S.146, H.289, W.290 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Q.34, D:Q.34, D:G.67, D:E.89, D:E.89, D:A.90, D:S.91, D:V.117, D:E.118, D:E.132, D:E.132, D:M.134, D:M.134, D:W.290 Water bridges: D:R.15, D:G.71, D:E.132 Salt bridges: D:R.43, D:E.132 pi-Stacking: D:F.25, D:F.25

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

EDO.2: 6 residues within 4Å: Chain A: D.40, L.287, T.288, H.289, Y.291, Y.351 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain B: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain B: P.248, F.249, K.250, S.310, G.311, T.312 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.249, B:T.312 EDO.15: 3 residues within 4Å: Chain C: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.16: 6 residues within 4Å: Chain C: D.40, L.287, T.288, H.289, Y.291, Y.351 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.39, C:D.40 EDO.20: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.21: 6 residues within 4Å: Chain D: Q.23, Y.24, F.27, Y.28, E.141, K.345 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.23

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

PEG.3: 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)

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 13 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, M.134, G.135, Y.136, N.140, E.141, H.289, W.290, K.345 Ligands: 6D4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.28, A:W.290 Water bridges: A:Y.136, A:E.141 PG4.5: 3 residues within 4Å: Chain A: Q.330, K.337, S.339 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.337 PG4.13: 13 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, G.135, Y.136, N.140, E.141, H.289, W.290, K.345, N.346 Ligands: 6D4.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.23, B:H.289, B:K.345 Water bridges: B:N.140

2 x M2M: 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE(Non-covalent)

M2M.6: 6 residues within 4Å: Chain A: G.158, N.159, L.235, I.271, G.272, S.273 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.159 M2M.18: 11 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, G.135, Y.136, N.140, E.141, H.289, W.290, K.345 No protein-ligand interaction detected (PLIP)

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

DXE.7: 2 residues within 4Å: Chain A: W.278, S.280 No protein-ligand interaction detected (PLIP) DXE.11: 8 residues within 4Å: Chain B: D.332, Q.333, T.334, G.335 Chain C: Q.48, L.52, Q.79 Chain D: G.195 No protein-ligand interaction detected (PLIP) DXE.12: 7 residues within 4Å: Chain B: N.36, Q.39, D.40, L.287, T.288, H.289, Y.291 No protein-ligand interaction detected (PLIP) DXE.17: 4 residues within 4Å: Chain C: N.159, I.271, G.272, S.273 No protein-ligand interaction detected (PLIP)

1 x SAO: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine(Non-covalent)

SAO.14: 28 residues within 4Å: Chain C: F.12, R.15, 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.143, S.146 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Q.34, C:G.67, C:G.69, C:E.89, C:E.89, C:A.90, C:S.91, C:V.117, C:E.118 Water bridges: C:R.15, C:G.71 Salt bridges: C:R.43 pi-Stacking: C:F.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cura, V. et al., Crystal structure of mouse CARM1 in complex with inhibitor SA0705. To Be Published

Release Date

2017-03-15

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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