SMTL ID : 5g02.1

Crystal Structure of zebrafish Protein Arginine Methyltransferase 2 with SFG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-hexamer

Ligands

6 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 21 residues within 4Å: Chain A: Y.13, F.14, Y.17, H.23, M.26, R.32, G.56, C.57, G.58, T.59, V.61, I.62, E.79, A.80, E.105, R.106, A.107, E.108, E.122, M.133, S.136 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.13, A:G.56, A:T.59, A:A.80, A:A.107, A:E.108, A:E.122, A:S.136 Salt bridges: A:R.32 pi-Stacking: A:F.14, A:F.14 SFG.7: 21 residues within 4Å: Chain B: Y.13, F.14, Y.17, H.23, M.26, R.32, G.56, C.57, G.58, T.59, V.61, I.62, E.79, A.80, E.105, R.106, A.107, E.108, E.122, M.133, S.136 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.13, B:G.56, B:T.59, B:A.80, B:A.107, B:E.108, B:E.122, B:S.136 Salt bridges: B:R.32 pi-Stacking: B:F.14, B:F.14 SFG.13: 21 residues within 4Å: Chain C: Y.13, F.14, Y.17, H.23, M.26, R.32, G.56, C.57, G.58, T.59, V.61, I.62, E.79, A.80, E.105, R.106, A.107, E.108, E.122, M.133, S.136 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.56, C:T.59, C:A.80, C:A.107, C:E.108, C:E.122, C:S.136 Salt bridges: C:R.32 pi-Stacking: C:F.14, C:F.14 SFG.19: 21 residues within 4Å: Chain D: Y.13, F.14, Y.17, H.23, M.26, R.32, G.56, C.57, G.58, T.59, V.61, I.62, E.79, A.80, E.105, R.106, A.107, E.108, E.122, M.133, S.136 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.56, D:T.59, D:A.80, D:A.107, D:E.108, D:E.122, D:S.136 Salt bridges: D:R.32 pi-Stacking: D:F.14, D:F.14 SFG.25: 21 residues within 4Å: Chain E: Y.13, F.14, Y.17, H.23, M.26, R.32, G.56, C.57, G.58, T.59, V.61, I.62, E.79, A.80, E.105, R.106, A.107, E.108, E.122, M.133, S.136 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:Y.13, E:G.56, E:T.59, E:A.80, E:A.107, E:E.108, E:E.122, E:S.136 Salt bridges: E:R.32 pi-Stacking: E:F.14, E:F.14 SFG.31: 21 residues within 4Å: Chain F: Y.13, F.14, Y.17, H.23, M.26, R.32, G.56, C.57, G.58, T.59, V.61, I.62, E.79, A.80, E.105, R.106, A.107, E.108, E.122, M.133, S.136 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.56, F:T.59, F:A.80, F:A.107, F:E.108, F:E.122, F:S.136 Salt bridges: F:R.32 pi-Stacking: F:F.14, F:F.14

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

MES.2: 9 residues within 4Å: Chain A: Y.13, N.16, Y.17, L.22, G.125, N.126, F.130, E.131, W.281 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.16, A:M.124, A:N.126, A:N.126 Salt bridges: A:E.131 MES.3: 7 residues within 4Å: Chain A: Q.9, E.12, Y.13, E.131, R.314, H.315, R.341 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.9 Salt bridges: A:E.12, A:H.315, A:R.341 MES.8: 9 residues within 4Å: Chain B: Y.13, N.16, Y.17, L.22, G.125, N.126, F.130, E.131, W.281 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.16, B:M.124, B:N.126, B:N.126 Salt bridges: B:E.131 MES.9: 7 residues within 4Å: Chain B: Q.9, E.12, Y.13, E.131, R.314, H.315, R.341 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.9 Salt bridges: B:E.12, B:H.315, B:R.341 MES.14: 9 residues within 4Å: Chain C: Y.13, N.16, Y.17, L.22, G.125, N.126, F.130, E.131, W.281 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.16, C:M.124, C:N.126, C:N.126 Salt bridges: C:E.131 MES.15: 7 residues within 4Å: Chain C: Q.9, E.12, Y.13, E.131, R.314, H.315, R.341 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.9 Salt bridges: C:E.12, C:H.315, C:R.341 MES.20: 9 residues within 4Å: Chain D: Y.13, N.16, Y.17, L.22, G.125, N.126, F.130, E.131, W.281 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.16, D:M.124, D:N.126, D:N.126 Salt bridges: D:E.131 MES.21: 7 residues within 4Å: Chain D: Q.9, E.12, Y.13, E.131, R.314, H.315, R.341 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.9 Salt bridges: D:E.12, D:H.315, D:R.341 MES.26: 9 residues within 4Å: Chain E: Y.13, N.16, Y.17, L.22, G.125, N.126, F.130, E.131, W.281 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.16, E:M.124, E:N.126, E:N.126 Salt bridges: E:E.131 MES.27: 7 residues within 4Å: Chain E: Q.9, E.12, Y.13, E.131, R.314, H.315, R.341 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.9 Salt bridges: E:E.12, E:H.315, E:R.341 MES.32: 9 residues within 4Å: Chain F: Y.13, N.16, Y.17, L.22, G.125, N.126, F.130, E.131, W.281 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.16, F:M.124, F:N.126, F:N.126 Salt bridges: F:E.131 MES.33: 7 residues within 4Å: Chain F: Q.9, E.12, Y.13, E.131, R.314, H.315, R.341 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.9 Salt bridges: F:E.12, F:H.315, F:R.341

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

EDO.4: 2 residues within 4Å: Chain A: Q.188, Q.192 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain A: T.219, I.225 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain B: Q.188, Q.192 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain B: T.219, I.225 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain C: Q.188, Q.192 No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Chain C: T.219, I.225 No protein-ligand interaction detected (PLIP) EDO.22: 2 residues within 4Å: Chain D: Q.188, Q.192 No protein-ligand interaction detected (PLIP) EDO.23: 2 residues within 4Å: Chain D: T.219, I.225 No protein-ligand interaction detected (PLIP) EDO.28: 2 residues within 4Å: Chain E: Q.188, Q.192 No protein-ligand interaction detected (PLIP) EDO.29: 2 residues within 4Å: Chain E: T.219, I.225 No protein-ligand interaction detected (PLIP) EDO.34: 2 residues within 4Å: Chain F: Q.188, Q.192 No protein-ligand interaction detected (PLIP) EDO.35: 2 residues within 4Å: Chain F: T.219, I.225 No protein-ligand interaction detected (PLIP)

6 x LI: LITHIUM ION(Non-covalent)

LI.6: 5 residues within 4Å: Chain A: D.6 Chain B: D.6 Chain E: D.6 Ligands: LI.12, LI.30 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: B:D.6, A:D.6, E:D.6, H2O.1, H2O.1 LI.12: 5 residues within 4Å: Chain A: D.6 Chain B: D.6 Chain E: D.6 Ligands: LI.6, LI.30 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: B:D.6, A:D.6, E:D.6, H2O.1, H2O.1 LI.18: 5 residues within 4Å: Chain C: D.6 Chain D: D.6 Chain F: D.6 Ligands: LI.24, LI.36 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: D:D.6, C:D.6, F:D.6, H2O.2, H2O.2 LI.24: 5 residues within 4Å: Chain C: D.6 Chain D: D.6 Chain F: D.6 Ligands: LI.18, LI.36 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: D:D.6, C:D.6, F:D.6, H2O.2, H2O.2 LI.30: 5 residues within 4Å: Chain A: D.6 Chain B: D.6 Chain E: D.6 Ligands: LI.6, LI.12 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:D.6, B:D.6, E:D.6, H2O.1, H2O.1 LI.36: 5 residues within 4Å: Chain C: D.6 Chain D: D.6 Chain F: D.6 Ligands: LI.18, LI.24 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.6, F:D.6, C:D.6, H2O.2, H2O.2

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

PROTEIN ARGININE METHYLTRANSFERASE 2