SMTL ID : 5fwd.1

Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 with CP2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GJV: 9-(7-{[amino(iminio)methyl]amino}-5,6,7-trideoxy-beta-D-ribo-heptofuranosyl)-9H-purin-6-amine(Non-covalent)

GJV.1: 20 residues within 4Å: Chain A: Y.115, F.116, Y.119, H.125, M.128, G.158, E.181, A.182, S.183, Q.207, K.208, V.209, E.210, E.224, W.225, M.226, G.227, E.233, M.235, S.238 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.119 Hydrogen bonds: A:Y.119, A:G.158, A:A.182, A:S.183, A:S.183, A:S.183, A:V.209, A:E.210, A:M.226, A:M.226, A:S.238 Water bridges: A:T.228, A:T.228 Salt bridges: A:E.224, A:E.233 pi-Stacking: A:F.116 GJV.12: 20 residues within 4Å: Chain B: Y.115, F.116, Y.119, H.125, M.128, G.158, E.181, A.182, S.183, Q.207, K.208, V.209, E.210, E.224, W.225, M.226, G.227, E.233, M.235, S.238 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.119 Hydrogen bonds: B:G.158, B:A.182, B:S.183, B:S.183, B:S.183, B:V.209, B:E.210, B:M.226, B:M.226, B:S.238 Water bridges: B:Y.119, B:Y.119, B:T.228, B:T.228 Salt bridges: B:E.224, B:E.233 pi-Stacking: B:F.116

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

PG4.2: 5 residues within 4Å: Chain A: D.151, 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 PG4.13: 5 residues within 4Å: Chain B: D.151, 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

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

EDO.3: 2 residues within 4Å: Chain A: R.300, W.445 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.300 EDO.4: 2 residues within 4Å: Chain A: P.376, H.378 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.380 EDO.5: 5 residues within 4Å: Chain A: E.114, Y.115, F.232, R.416, H.417 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.114 Water bridges: A:S.118 EDO.6: 3 residues within 4Å: Chain A: L.377, H.378 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: Y.359, S.373, H.378 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.359, A:Y.359, A:S.373, A:H.378 EDO.8: 4 residues within 4Å: Chain A: L.320, T.334, M.335, R.336 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.336 EDO.14: 2 residues within 4Å: Chain B: R.300, W.445 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.300 EDO.15: 2 residues within 4Å: Chain B: P.376, H.378 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.380 EDO.16: 5 residues within 4Å: Chain B: E.114, Y.115, F.232, R.416, H.417 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.114, B:E.114 Water bridges: B:S.118 EDO.17: 3 residues within 4Å: Chain B: L.377, H.378 Ligands: EDO.18 No protein-ligand interaction detected (PLIP) EDO.18: 4 residues within 4Å: Chain B: Y.359, S.373, H.378 Ligands: EDO.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.359, B:S.373, B:H.378 EDO.19: 4 residues within 4Å: Chain B: L.320, T.334, M.335, R.336 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.336

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

CL.9: 4 residues within 4Å: Chain A: G.375, P.376, L.377, H.378 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: G.375, P.376, L.377, H.378 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.10: 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.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.21: 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.14, H2O.14 CA.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

2017-03-01

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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