SMTL ID : 6dub.2 (1 other biounit)

Crystal structure of a methyltransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x 5JP- PRO- LYS- ARG- ILE: RCC1(Non-covalent)

5JP-PRO-LYS-ARG-ILE.1: 18 residues within 4Å: Chain A: M.30, M.31, G.32, F.34, W.135, N.167, D.176, D.179, S.181, F.209, Q.212, C.213, I.214 Ligands: SAH.2, GOL.3, UNX.19, UNX.23, UNX.26 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.34, A:F.34, A:F.34, A:W.135, A:F.209, A:I.214 Hydrogen bonds: A:N.167, A:D.176, A:S.181, A:Q.212, A:I.214 Water bridges: A:N.167

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

SAH.2: 22 residues within 4Å: Chain A: Y.20, M.30, G.68, S.69, G.70, R.73, V.74, D.90, M.91, M.92, F.95, Y.116, S.117, L.118, Q.119, Q.134, W.135, V.136, H.139, L.140 Ligands: 5JP-PRO-LYS-ARG-ILE.1, UNX.13 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.68, A:G.70, A:M.91, A:L.118, A:Q.119 Water bridges: A:V.74, A:S.117 Salt bridges: A:R.73

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: W.135, V.136, S.137, G.138, H.139, D.166, D.179, S.181 Ligands: 5JP-PRO-LYS-ARG-ILE.1, 5JP-PRO-LYS-ARG-ILE.1, UNX.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.138, A:D.166, A:D.179

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

UNX.4: 8 residues within 4Å: Chain A: I.133, Q.134, W.135, V.136, S.137, L.164, K.165, D.166 Ligand excluded by PLIP UNX.5: 3 residues within 4Å: Chain A: T.122, D.154 Ligands: UNX.15 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: A.169, R.170, P.215 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: L.103, K.106 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: L.80, F.83, K.106, K.109 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: N.33, E.36 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: G.107, V.110, Y.113 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: E.36, P.210 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: Q.43, Q.46, R.50 Ligand excluded by PLIP UNX.13: 5 residues within 4Å: Chain A: D.66, C.67, W.132, Q.134 Ligands: SAH.2 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: K.47, R.50, K.51 Ligand excluded by PLIP UNX.15: 6 residues within 4Å: Chain A: T.122, P.123, R.151, D.154, G.155 Ligands: UNX.5 Ligand excluded by PLIP UNX.16: 6 residues within 4Å: Chain A: Y.20, Q.21, V.23, M.92, S.94, F.95 Ligand excluded by PLIP UNX.17: 1 residues within 4Å: Chain A: Y.102 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: R.170, K.205 Ligand excluded by PLIP UNX.19: 5 residues within 4Å: Chain A: F.19, Y.20, D.179 Ligands: 5JP-PRO-LYS-ARG-ILE.1, GOL.3 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain A: G.8, Q.11, F.12 Ligand excluded by PLIP UNX.21: 5 residues within 4Å: Chain A: R.153, G.197, L.198, V.199, H.222 Ligand excluded by PLIP UNX.22: 5 residues within 4Å: Chain A: A.169, R.170, D.185, M.186, D.187 Ligand excluded by PLIP UNX.23: 6 residues within 4Å: Chain A: G.32, N.33, F.34 Ligands: 5JP-PRO-LYS-ARG-ILE.1, 5JP-PRO-LYS-ARG-ILE.1, 5JP-PRO-LYS-ARG-ILE.1 Ligand excluded by PLIP UNX.24: 3 residues within 4Å: Chain A: C.115, Y.116 Ligands: UNX.25 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain A: Y.113, H.114, C.115, Y.116 Ligands: UNX.24 Ligand excluded by PLIP UNX.26: 3 residues within 4Å: Chain A: F.34 Ligands: 5JP-PRO-LYS-ARG-ILE.1, 5JP-PRO-LYS-ARG-ILE.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2. Commun Biol (2018)

Release Date

2018-07-25

Peptides

Alpha N-terminal protein methyltransferase 1B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Alpha N-terminal protein methyltransferase 1B

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