SMTL ID : 5lgr.1

Crystal structure of mouse CARM1 in complex with ligand P1C3u

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-4-4-mer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: N.318, K.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.319

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

EDO.2: 3 residues within 4Å: Chain A: D.267, W.278, S.280 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.267, A:D.267 EDO.3: 5 residues within 4Å: Chain A: P.283, T.284, E.285, P.286, L.287 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.287 EDO.5: 4 residues within 4Å: Chain B: D.267, W.278, S.280, E.285 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain C: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain D: D.267, W.278, S.280 No protein-ligand interaction detected (PLIP) EDO.12: 8 residues within 4Å: Chain A: Y.291, F.349, Y.351 Chain E: A.11, A.12 Chain F: F.1 Ligands: LPD.11, ACE.13 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.12

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

DXE.4: 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)

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

PG6.6: 9 residues within 4Å: Chain B: R.9, S.10, E.118, E.119, V.120, S.121, L.122, K.152, Y.153 No protein-ligand interaction detected (PLIP)

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

PEG.8: 8 residues within 4Å: Chain B: D.332, Q.333, T.334, G.335 Chain C: Q.48, L.52, Q.53, Q.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.79

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(Covalent)(Non-covalent)

QVR.10: 23 residues within 4Å: Chain A: 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 E: R.9 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.34, A:G.67, A:G.69, A:E.89, A:E.89, A:A.90, A:V.117, A:E.118 Water bridges: A:R.15 pi-Stacking: A:F.25 QVR.14: 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 Chain F: R.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.28 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:S.131 pi-Stacking: B:F.25 QVR.17: 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 Chain G: R.9 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.28 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.19: 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.9 11 PLIP interactions: 11 interactions with chain D 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

4 x LPD: L-PROLINAMIDE(Covalent)(Non-covalent)

LPD.11: 8 residues within 4Å: Chain A: L.287, T.288, H.289, Y.291, Y.351 Chain E: A.11, A.12 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.287 LPD.15: 6 residues within 4Å: Chain B: L.287, T.288, H.289, Y.291 Chain F: A.11, A.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.287 LPD.16: 6 residues within 4Å: Chain C: L.287, T.288, H.289, Y.291 Chain G: A.11, A.12 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.287 LPD.20: 7 residues within 4Å: Chain D: L.287, T.288, H.289, Y.291, Y.351 Chain H: A.11, A.12 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.287, D:L.287, D:Y.291, D:Y.351

2 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.13: 4 residues within 4Å: Chain E: A.11 Chain F: F.1, Q.2 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.2 Water bridges: F:Q.2 ACE.18: 3 residues within 4Å: Chain G: A.11 Chain H: F.1, Q.2 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.2

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
E

F
F

G
G

H
H

Histone-arginine methyltransferase CARM1

Polyadenylate-binding protein 1

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