SMTL ID : 5lgs.1

Crystal structure of mouse CARM1 in complex with ligand P2C3u

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x ALA- ALA- PRO- ARG- PRO- PRO- PHE- SER: Polyadenylate-binding protein 1(Non-covalent)

ALA-ALA-PRO-ARG-PRO-PRO-PHE-SER.1: 26 residues within 4Å: Chain A: Q.23, Y.24, F.27, Y.28, N.36, M.37, D.40, Y.41, R.43, E.132, M.134, G.135, Y.136, N.140, E.141, V.215, L.287, T.288, H.289, W.290, Y.291, K.345, N.346, P.347, F.349 Ligands: QVR.14 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.27, A:F.27, A:Y.28, A:H.289, A:Y.291, A:F.349 Hydrogen bonds: A:Q.23, A:Y.28, A:N.36, A:N.36, A:E.132, A:E.141, A:H.289, A:Y.291 Water bridges: A:N.140, A:N.140, A:Y.291, A:Y.351 Salt bridges: A:E.132, A:E.141 ALA-ALA-PRO-ARG-PRO-PRO-PHE-SER.2: 30 residues within 4Å: Chain A: Q.23, Q.26, F.27, Y.30 Chain B: Y.24, F.27, Y.28, N.36, M.37, Q.39, D.40, Y.41, R.43, E.132, M.134, G.135, Y.136, N.140, E.141, V.215, L.287, T.288, H.289, W.290, Y.291, K.345, N.346, P.347, F.349 Ligands: QVR.15 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.24, B:F.27, B:F.27, B:Y.28, B:H.289, B:Y.291, B:P.347, B:F.349 Hydrogen bonds: B:Y.28, B:N.36, B:N.36, B:E.132, B:N.140, B:E.141, B:H.289, B:Y.291 Water bridges: B:Y.291 Salt bridges: B:E.132, B:E.141 ALA-ALA-PRO-ARG-PRO-PRO-PHE-SER.3: 25 residues within 4Å: Chain C: Y.24, F.27, Y.28, N.36, M.37, D.40, Y.41, R.43, E.132, M.134, G.135, Y.136, N.140, E.141, V.215, L.287, T.288, H.289, W.290, Y.291, K.345, N.346, P.347, F.349 Ligands: QVR.16 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.27, C:F.27, C:Y.28, C:H.289, C:Y.291, C:F.349 Hydrogen bonds: C:Y.28, C:N.36, C:N.36, C:E.132, C:H.289, C:Y.291 Water bridges: C:N.140 Salt bridges: C:E.132, C:E.141 ALA-ALA-PRO-ARG-PRO-PRO-PHE-SER.4: 25 residues within 4Å: Chain D: Y.24, F.27, Y.28, N.36, M.37, Q.39, D.40, Y.41, R.43, E.132, M.134, G.135, Y.136, N.140, E.141, V.215, L.287, T.288, H.289, W.290, Y.291, K.345, P.347, F.349 Ligands: QVR.17 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:Y.24, D:F.27, D:H.289, D:Y.291, D:F.349, D:F.349 Hydrogen bonds: D:Y.28, D:N.36, D:N.36, D:E.132, D:N.140, D:H.289, D:Y.291 Salt bridges: D:E.132, D:E.141

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: A.317, N.318, K.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.319 Water bridges: A:E.17

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

DXE.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 DXE.8: 4 residues within 4Å: Chain B: D.267, W.278, S.280, E.285 No protein-ligand interaction detected (PLIP) DXE.13: 9 residues within 4Å: Chain A: Q.48, L.52, Q.79 Chain B: G.195 Chain D: D.332, Q.333, T.334, G.335, K.337 No protein-ligand interaction detected (PLIP)

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

PEG.7: 4 residues within 4Å: Chain A: D.267, W.278, S.280, E.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.285 Water bridges: A:S.280

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

PG4.9: 6 residues within 4Å: Chain B: R.9, S.10, E.118, E.119, V.120, K.152 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.152, B:K.152

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

EDO.10: 3 residues within 4Å: Chain C: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain B: D.332, T.334, G.335 Chain C: Q.48, L.52, Q.79 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.48, B:D.332 EDO.12: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP)

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

QVR.14: 22 residues within 4Å: Chain A: F.12, R.15, Y.24, F.25, Y.28, 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, E.141, M.143, S.146 Ligands: ALA-ALA-PRO-ARG-PRO-PRO-PHE-SER.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.67, A:G.69, A:E.89, A:E.89, A:A.90, A:S.91, A:V.117, A:E.118 Water bridges: A:R.15 pi-Stacking: A:F.25 QVR.15: 23 residues within 4Å: Chain B: 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, E.141, M.143, S.146 Ligands: PRO-ALA-ALA-PRO-ARG-PRO-PRO-PHE-SER.2 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.67, B:G.69, B:E.89, B:E.89, B:A.90, B:V.117, B:E.118 Water bridges: B:R.15, B:Q.34, B:Q.34 pi-Stacking: B:F.25 QVR.16: 23 residues within 4Å: Chain C: 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, E.141, M.143, S.146 Ligands: ALA-ALA-PRO-ARG-PRO-PRO-PHE-SER.3 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: 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:Q.34 pi-Stacking: C:F.25 QVR.17: 23 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, E.141, M.143, S.146 Ligands: ALA-ALA-PRO-ARG-PRO-PRO-PHE-SER.4 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.67, D:G.69, D:E.89, D:E.89, D:A.90, D:S.91, D:V.117, D:E.118 Water bridges: D:R.15, D:Q.34, D:Q.34 pi-Stacking: D:F.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Haren, M.J. et al., Transition state mimics are valuable mechanistic probes for structural studies with the arginine methyltransferase CARM1. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-03-22

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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