SMTL ID : 5fub.1

Crystal Structure of zebrafish Protein Arginine Methyltransferase 2 catalytic domain with SAH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: Y.9, F.10, Y.13, H.19, M.22, R.28, G.52, C.53, G.54, V.57, I.58, E.75, A.76, E.101, R.102, A.103, E.104, E.118, M.129, S.132 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.9, A:G.52, A:G.54, A:A.76, A:A.103, A:E.104, A:S.132 Water bridges: A:G.56, A:R.310, A:R.310, A:R.310 Salt bridges: A:R.28 pi-Stacking: A:F.10, A:F.10 SAH.10: 20 residues within 4Å: Chain B: Y.9, F.10, Y.13, H.19, M.22, R.28, G.52, C.53, G.54, V.57, I.58, E.75, A.76, E.101, R.102, A.103, E.104, E.118, M.129, S.132 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.52, B:G.54, B:A.76, B:A.103, B:E.104, B:S.132 Water bridges: B:G.56, B:R.310, B:R.310, B:R.310 Salt bridges: B:R.28 pi-Stacking: B:F.10, B:F.10

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 10 residues within 4Å: Chain A: Y.9, N.12, Y.13, L.18, G.121, N.122, F.126, E.127, R.337 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.12, A:N.122, A:N.122, A:E.127 Salt bridges: A:E.127, A:R.337 MES.11: 10 residues within 4Å: Chain B: Y.9, N.12, Y.13, L.18, G.121, N.122, F.126, E.127, R.337 Ligands: EDO.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.12, B:N.122, B:N.122, B:E.127 Salt bridges: B:E.127, B:R.337

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

CL.3: 3 residues within 4Å: Chain A: R.33, F.61 Chain B: Y.176 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: Y.176 Chain B: R.33, F.61 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: A.80, E.84, Q.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.100 NA.9: 2 residues within 4Å: Chain A: C.153, D.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.212 NA.13: 3 residues within 4Å: Chain B: A.80, E.84, Q.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.84 NA.18: 2 residues within 4Å: Chain B: C.153, D.212 No protein-ligand interaction detected (PLIP)

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

EDO.5: 6 residues within 4Å: Chain A: Q.5, E.8, Y.9, N.12, E.127 Ligands: MES.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.8, A:E.8, A:N.12, A:E.127 EDO.6: 4 residues within 4Å: Chain A: H.200, S.272, E.273, I.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.274 Water bridges: A:P.270, A:S.272 EDO.7: 3 residues within 4Å: Chain A: G.1, D.6, D.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.1, A:D.6, A:D.7 Water bridges: A:E.8 EDO.8: 5 residues within 4Å: Chain A: T.155, P.210, W.249, N.267, Y.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.249, A:N.267 Water bridges: A:Y.271 EDO.14: 6 residues within 4Å: Chain B: Q.5, E.8, Y.9, N.12, E.127 Ligands: MES.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.8, B:N.12 EDO.15: 4 residues within 4Å: Chain B: H.200, S.272, E.273, I.274 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.274 Water bridges: B:P.270, B:S.272 EDO.16: 3 residues within 4Å: Chain B: G.1, D.6, D.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.1, B:D.6, B:D.7 Water bridges: B:E.8 EDO.17: 5 residues within 4Å: Chain B: T.155, P.210, W.249, N.267, Y.271 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.249, B:N.267 Water bridges: B:Y.271

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 METHYLTRANSFERASE 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PROTEIN ARGININE METHYLTRANSFERASE 2