SMTL ID : 5ful.1

Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 with SAH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: Y.115, F.116, Y.119, H.125, M.128, R.134, G.158, C.159, G.160, I.163, I.164, E.181, A.182, Q.207, K.208, V.209, E.210, E.224, M.235, S.238 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:H.125, A:G.158, A:A.182, A:V.209, A:E.210, A:S.238 Water bridges: A:Y.115, A:T.161, A:G.162, A:E.224, A:R.416 Salt bridges: A:R.134 pi-Stacking: A:F.116 SAH.8: 20 residues within 4Å: Chain B: Y.115, F.116, Y.119, H.125, M.128, R.134, G.158, C.159, G.160, I.163, I.164, E.181, A.182, Q.207, K.208, V.209, E.210, E.224, M.235, S.238 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:H.125, B:G.158, B:A.182, B:V.209, B:E.210, B:S.238 Water bridges: B:T.161, B:G.162, B:E.224, B:R.416 Salt bridges: B:R.134 pi-Stacking: B:F.116

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.4 CA.3: 1 residues within 4Å: Chain A: M.226 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:M.226, H2O.1, H2O.5, H2O.5, H2O.6 CA.9: 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.16 CA.10: 1 residues within 4Å: Chain B: M.226 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:M.226, H2O.13, H2O.17, H2O.17, H2O.17

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

PG4.4: 6 residues within 4Å: Chain A: K.152, D.219, K.248, D.250, L.363, E.364 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.152, A:K.248, A:K.248, A:D.250 PG4.11: 6 residues within 4Å: Chain B: K.152, D.219, K.248, D.250, L.363, E.364 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.152, B:K.248, B:K.248, B:D.250 Water bridges: B:D.219

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

CL.5: 4 residues within 4Å: Chain A: G.375, P.376, L.377, H.378 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: G.375, P.376, L.377, H.378 Ligand excluded by PLIP

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

EDO.6: 7 residues within 4Å: Chain A: Q.111, E.114, F.232, H.417, W.445, W.446 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.111 EDO.7: 4 residues within 4Å: Chain A: R.300, W.445, W.446 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.300, A:R.300 EDO.13: 7 residues within 4Å: Chain B: Q.111, E.114, F.232, H.417, W.445, W.446 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.111 EDO.14: 4 residues within 4Å: Chain B: R.300, W.445, W.446 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.300, B:R.300

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

2016-11-09

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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