SMTL ID : 5lgq.1

Crystal structure of mouse CARM1 in complex with ligand P2C3s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

hetero-4-4-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: N.159, I.271, G.272, S.273 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.159 EDO.7: 3 residues within 4Å: Chain B: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.8: 8 residues within 4Å: Chain B: Y.230, T.231, V.232, N.233, A.237, D.241, L.242, I.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.230, B:D.241 EDO.9: 6 residues within 4Å: Chain B: I.220, P.283, T.284, E.285, P.286, L.287 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.287 EDO.10: 3 residues within 4Å: Chain C: D.267, W.278, S.280 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.267 EDO.11: 6 residues within 4Å: Chain C: F.182, V.206, D.207, F.210, Q.298 Ligands: PEG.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.207, C:Q.298 Water bridges: C:S.299 EDO.13: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP)

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

PEG.2: 4 residues within 4Å: Chain A: D.267, W.278, S.280, E.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.285 PEG.3: 8 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.48, A:Q.79 Water bridges: A:L.52 PEG.12: 7 residues within 4Å: Chain C: F.182, Y.189, R.202, G.203, V.206, D.207 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.202, C:D.207 Water bridges: C:R.202 PEG.14: 8 residues within 4Å: Chain B: Y.189, S.199, A.200, R.202, G.203 Chain D: Y.189, R.202, G.203 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.202 Water bridges: D:G.203

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

DXE.4: 6 residues within 4Å: Chain A: F.182, Y.189, S.199, R.202, G.203, V.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.202 Water bridges: A:R.202

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

PG6.5: 4 residues within 4Å: Chain A: V.328, Q.330, K.337, S.339 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.337

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

SO4.6: 3 residues within 4Å: Chain A: N.318, K.319, R.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.319, A:R.320

4 x 8ZB: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol(Non-covalent)

8ZB.15: 24 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, E.141, M.143, S.146 Chain E: R.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.28 Hydrogen bonds: B:G.67, B:E.89, B:E.89, B:A.90, B:V.117, B:E.118 Water bridges: B:Q.34, B:S.131 pi-Stacking: B:F.25 8ZB.16: 24 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, E.141, M.143, S.146 Chain F: R.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.28 Hydrogen bonds: A:G.67, A:E.89, A:E.89, A:A.90, A:V.117, A:E.118 Water bridges: A:R.15, A:Q.34, A:S.131 pi-Stacking: A:F.25 8ZB.17: 24 residues within 4Å: Chain C: 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, E.141, M.143, S.146 Chain G: R.5 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 8ZB.18: 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 Chain H: R.5 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.28 Hydrogen bonds: D:G.67, D:G.69, D:E.89, D:E.89, D:A.90, 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
Polyadenylate-binding protein 1: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
E

G
G

H
H

Histone-arginine methyltransferase CARM1

Polyadenylate-binding protein 1

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