SMTL ID : 5k8w.1

Crystal structure of mouse CARM1 in complex with inhibitor U2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x GJV: 9-(7-{[amino(iminio)methyl]amino}-5,6,7-trideoxy-beta-D-ribo-heptofuranosyl)-9H-purin-6-amine(Non-covalent)

GJV.1: 26 residues within 4Å: Chain A: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, G.67, C.68, 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:E.89, A:E.89, A:A.90, A:S.91, A:S.91, A:V.117, A:E.118, A:E.132, 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 GJV.9: 24 residues within 4Å: Chain B: 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 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Y.28, B:Y.28, 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:E.132 Water bridges: B:R.15, B:Q.34, B:R.43 Salt bridges: B:E.132, B:E.141 pi-Stacking: B:F.25 GJV.13: 26 residues within 4Å: Chain C: F.12, R.15, Y.24, F.25, Y.28, Q.34, M.37, G.67, C.68, 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 C Hydrophobic interactions: C:Y.28 Hydrogen bonds: C:Y.28, 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 Water bridges: C:R.15, C:W.290, C:W.290 Salt bridges: C:E.132, C:E.141 pi-Stacking: C:F.25 GJV.20: 24 residues within 4Å: Chain D: F.12, R.15, Y.24, F.25, Y.28, Q.34, 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:Y.28, D:G.67, D:G.69, D:E.89, D:E.89, D:A.90, D:S.91, D:S.91, D:V.117, D:E.118, D:E.132 Water bridges: D:R.15, D:Q.34, D:Q.34 Salt bridges: D:E.132, D:E.141 pi-Stacking: D:F.25

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

DXE.2: 7 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, Y.136, N.140, E.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.28 DXE.3: 6 residues within 4Å: Chain A: Q.48, L.52 Chain D: D.332, Q.333, T.334, G.335 No protein-ligand interaction detected (PLIP) DXE.14: 5 residues within 4Å: Chain C: Q.23, Y.24, F.27, Y.28, E.141 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.345 DXE.15: 3 residues within 4Å: Chain C: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) DXE.19: 4 residues within 4Å: Chain C: N.159, I.271, G.272, S.273 No protein-ligand interaction detected (PLIP) DXE.21: 4 residues within 4Å: Chain D: D.267, W.278, S.280, E.285 No protein-ligand interaction detected (PLIP)

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

EDO.4: 3 residues within 4Å: Chain A: D.267, W.278, S.280 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.280 EDO.5: 4 residues within 4Å: Chain A: P.283, T.284, E.285, P.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.283 EDO.6: 6 residues within 4Å: Chain A: D.40, L.287, T.288, H.289, Y.291, Y.351 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.291 Water bridges: A:Q.39 EDO.10: 7 residues within 4Å: Chain B: D.332, Q.333, T.334, G.335 Chain C: Q.48, L.52, Q.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.79 EDO.11: 6 residues within 4Å: Chain B: Q.23, Y.24, F.27, Y.28, E.141, K.345 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.28, B:N.140, B:E.141 EDO.16: 7 residues within 4Å: Chain C: K.151, K.152, L.154, K.155, P.156, G.158, L.235 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.151, C:P.156 Water bridges: C:G.158 EDO.17: 5 residues within 4Å: Chain C: D.40, L.287, T.288, H.289, Y.291 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.291, C:Y.291 Water bridges: C:Q.39, C:D.40, C:D.40, C:L.287 EDO.18: 5 residues within 4Å: Chain C: P.283, T.284, E.285, P.286, L.287 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.284 Water bridges: C:L.287 EDO.22: 7 residues within 4Å: Chain D: Q.23, Y.24, F.27, Y.28, N.140, E.141, K.345 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.23, D:Q.23, D:E.141 Water bridges: D:N.140

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

PG4.7: 3 residues within 4Å: Chain A: V.328, Q.330, K.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.337

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

PEG.8: 7 residues within 4Å: Chain A: S.157, G.158, N.159, L.235, I.271, G.272, S.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.158, A:G.272 Water bridges: A:N.159, A:N.159 PEG.12: 4 residues within 4Å: Chain B: D.267, W.278, S.280, E.285 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cura, V. et al., Crystal structure of mouse CARM1 in complex with inhibitor U2. To Be Published

Release Date

2017-06-21

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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