SMTL ID : 5jmq.1

Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 with CP3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

PG4.1: 5 residues within 4Å: Chain A: K.150, K.152, D.219, D.250, L.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.152, A:D.219, A:D.250 PG4.9: 5 residues within 4Å: Chain B: K.150, K.152, D.219, D.250, L.363 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.152, B:D.219, B:D.250 Water bridges: B:D.219

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

EDO.2: 2 residues within 4Å: Chain A: H.378, P.379 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.377 EDO.3: 6 residues within 4Å: Chain A: Q.111, Y.115, F.232, E.233, R.416 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.111 EDO.4: 2 residues within 4Å: Chain A: R.300, W.445 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.300, A:R.300 EDO.5: 5 residues within 4Å: Chain A: Q.111, E.114, H.417, W.446 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.111, A:Q.111 EDO.10: 2 residues within 4Å: Chain B: H.378, P.379 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.377 EDO.11: 6 residues within 4Å: Chain B: Q.111, Y.115, F.232, E.233, R.416 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.111 EDO.12: 2 residues within 4Å: Chain B: R.300, W.445 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.300, B:R.300 EDO.13: 5 residues within 4Å: Chain B: Q.111, E.114, H.417, W.446 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.111, B:Q.111

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 2 residues within 4Å: Chain A: G.197, D.200 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.197, A:D.200, A:D.200, H2O.4, H2O.7 CA.14: 2 residues within 4Å: Chain B: G.197, D.200 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.197, B:D.200, B:D.200, H2O.16, H2O.19

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: G.375, P.376, L.377, H.378 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: G.375, P.376, L.377, H.378 Ligand excluded by PLIP

2 x 6LC: 9-[(5E)-7-carbamimidamido-5,6,7-trideoxy-beta-D-ribo-hept-5-enofuranosyl]-9H-purin-6-amine(Non-covalent)

6LC.8: 20 residues within 4Å: Chain A: Y.115, F.116, Y.119, H.125, M.128, G.158, G.160, E.181, A.182, S.183, Q.207, K.208, V.209, E.210, E.224, M.226, M.235, S.238, H.382, W.383 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.119, A:H.125, A:G.158, A:A.182, A:V.209, A:E.210, A:S.238, A:H.382 Water bridges: A:R.416 Salt bridges: A:E.224, A:E.233 pi-Stacking: A:F.116 6LC.16: 20 residues within 4Å: Chain B: Y.115, F.116, Y.119, H.125, M.128, G.158, G.160, E.181, A.182, S.183, Q.207, K.208, V.209, E.210, E.224, M.226, M.235, S.238, H.382, W.383 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.119, B:Y.119, B:H.125, B:G.158, B:A.182, B:V.209, B:E.210, B:S.238, B:H.382 Water bridges: B:R.416 Salt bridges: B:E.224, B:E.233 pi-Stacking: B:F.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cura, V. et al., Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors. Febs J. (2017)

Release Date

2017-05-10

Peptides

Protein arginine N-methyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein arginine N-methyltransferase 2

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