SMTL ID : 5e8r.1

Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 21 residues within 4Å: Chain A: Y.48, Y.49, Y.52, H.58, M.61, R.67, G.91, A.92, G.93, L.97, E.113, A.114, S.115, G.139, P.140, V.141, E.142, E.156, M.167, S.170 Ligands: 5L6.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.91, A:G.91, A:A.114, A:S.115, A:S.115, A:V.141, A:E.142, A:S.170 Salt bridges: A:R.67 pi-Stacking: A:Y.49 SAH.5: 24 residues within 4Å: Chain B: Y.48, Y.49, Y.52, H.58, M.61, R.67, G.91, A.92, G.93, T.94, I.96, L.97, E.113, A.114, S.115, G.139, P.140, V.141, E.142, E.156, M.167, S.170 Ligands: 5L6.6, UNX.18 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.58, B:G.91, B:G.93, B:A.114, B:V.141, B:E.142, B:S.170 Salt bridges: B:R.67 pi-Stacking: B:Y.49

2 x 5L6: N-methyl-N-({4-[4-(propan-2-yloxy)phenyl]-1H-pyrrol-3-yl}methyl)ethane-1,2-diamine(Non-covalent)

5L6.2: 14 residues within 4Å: Chain A: Y.48, C.51, Y.52, V.57, E.60, M.61, E.156, M.158, Y.160, H.164, E.165, H.318, W.319 Ligands: SAH.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.48, A:V.57, A:Y.160, A:E.165 Hydrogen bonds: A:E.60, A:E.156 Water bridges: A:Y.52 Salt bridges: A:E.156, A:E.165 5L6.6: 14 residues within 4Å: Chain B: Y.48, C.51, Y.52, V.57, E.60, M.61, E.156, M.158, Y.160, H.164, E.165, H.318, W.319 Ligands: SAH.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.48, B:V.57, B:Y.160 Hydrogen bonds: B:E.60, B:M.158 Water bridges: B:Y.52 Salt bridges: B:E.156, B:E.165

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

CL.3: 5 residues within 4Å: Chain A: S.189, A.190, E.191, V.295, T.296 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain B: S.189, A.190, E.191, Q.294, V.295, T.296 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: Y.49, S.53, S.115, A.116 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: R.122, V.134, H.135, V.136 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: L.326, N.327, Y.360 Ligand excluded by PLIP

9 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 1 residues within 4Å: Chain A: D.151 No protein-ligand interaction detected (PLIP) UNX.11: 6 residues within 4Å: Chain B: S.309, T.310, S.311, H.314, P.315, A.316 No protein-ligand interaction detected (PLIP) UNX.12: 1 residues within 4Å: Chain B: W.118 No protein-ligand interaction detected (PLIP) UNX.13: 3 residues within 4Å: Chain B: G.263, E.265, Q.266 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain B: F.193, W.292, S.311 No protein-ligand interaction detected (PLIP) UNX.15: 4 residues within 4Å: Chain B: D.64, R.65, V.66, A.316 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Chain B: A.249, R.250, S.279 No protein-ligand interaction detected (PLIP) UNX.17: 5 residues within 4Å: Chain B: W.292, F.293, T.310, W.319, K.320 No protein-ligand interaction detected (PLIP) UNX.18: 4 residues within 4Å: Chain B: H.58, I.62, T.94 Ligands: SAH.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eram, M.S. et al., A Potent, Selective, and Cell-Active Inhibitor of Human Type I Protein Arginine Methyltransferases. Acs Chem.Biol. (2016)

Release Date

2015-12-09

Peptides

Protein arginine N-methyltransferase 6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein arginine N-methyltransferase 6

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