SMTL ID : 6dub.1 (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, Q.212, C.213, I.214 Ligands: SAH.2, GOL.4, UNX.22, UNX.39, UNX.40, UNX.41 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.34, A:F.34, A:F.34, A:W.135, A:I.214 Hydrogen bonds: A:N.167, A:D.176, A:D.176, A:S.181, A:Q.212, A:I.214 Water bridges: A:N.167, A:D.179, A:D.179

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

SAH.2: 21 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.68, A:M.91, A:L.118, A:Q.119 Water bridges: A:S.117, A:Q.134 Salt bridges: A:R.73

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: S.39, I.42, Q.43, Q.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.43, A:Q.46, A:Q.46 GOL.4: 10 residues within 4Å: Chain A: W.135, V.136, S.137, G.138, D.166, N.167, D.179, S.181 Ligands: 5JP-PRO-LYS-ARG-ILE.1, 5JP-PRO-LYS-ARG-ILE.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.138, A:N.167, A:S.181 Water bridges: A:D.166, A:S.181, A:V.182

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

UNX.5: 3 residues within 4Å: Chain A: F.48, F.52, Q.203 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: I.6, G.8 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: K.205, Q.206, P.215, V.216 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: E.120, F.121, T.122 Ligand excluded by PLIP UNX.9: 5 residues within 4Å: Chain A: F.12, Y.13, A.16, H.139, S.180 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: P.210, E.211, C.213 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: T.26, E.27, E.28 Ligand excluded by PLIP UNX.12: 1 residues within 4Å: Chain A: K.17 Ligand excluded by PLIP UNX.13: 2 residues within 4Å: Chain A: Q.119, D.144 Ligand excluded by PLIP UNX.14: 1 residues within 4Å: Chain A: Q.43 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: T.141, D.142, K.143 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: N.33, E.36 Ligand excluded by PLIP UNX.17: 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.18: 2 residues within 4Å: Chain A: H.114, Y.116 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: P.124, F.125 Ligand excluded by PLIP UNX.20: 4 residues within 4Å: Chain A: E.9, T.141, K.143, D.144 Ligand excluded by PLIP UNX.21: 1 residues within 4Å: Chain A: Y.113 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain A: N.33, F.34 Ligands: 5JP-PRO-LYS-ARG-ILE.1, UNX.39 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Chain A: P.24, A.25 Ligand excluded by PLIP UNX.24: 1 residues within 4Å: Chain A: R.194 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain A: G.54, G.55, R.58, A.59, G.60 Ligand excluded by PLIP UNX.26: 3 residues within 4Å: Chain A: T.61, V.82, N.84 Ligand excluded by PLIP UNX.27: 4 residues within 4Å: Chain A: L.96, L.97, Q.100, Y.113 Ligand excluded by PLIP UNX.28: 4 residues within 4Å: Chain A: A.169, R.170, D.185, M.186 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain A: R.50, V.82 Ligand excluded by PLIP UNX.30: 2 residues within 4Å: Chain A: L.103, K.106 Ligand excluded by PLIP UNX.31: 5 residues within 4Å: Chain A: A.44, K.47, F.48, E.204, M.218 Ligand excluded by PLIP UNX.32: 2 residues within 4Å: Chain A: Q.11, R.15 Ligand excluded by PLIP UNX.33: 3 residues within 4Å: Chain A: R.15, L.18, F.19 Ligand excluded by PLIP UNX.34: 2 residues within 4Å: Chain A: R.15, L.177 Ligand excluded by PLIP UNX.35: 5 residues within 4Å: Chain A: R.153, G.197, L.198, V.199, H.222 Ligand excluded by PLIP UNX.36: 3 residues within 4Å: Chain A: N.159, G.160, H.222 Ligand excluded by PLIP UNX.37: 2 residues within 4Å: Chain A: E.36, P.210 Ligand excluded by PLIP UNX.38: 6 residues within 4Å: Chain A: Y.20, Q.21, V.23, M.92, S.94, F.95 Ligand excluded by PLIP UNX.39: 4 residues within 4Å: Chain A: F.34 Ligands: 5JP-PRO-LYS-ARG-ILE.1, 5JP-PRO-LYS-ARG-ILE.1, UNX.22 Ligand excluded by PLIP UNX.40: 1 residues within 4Å: Ligands: 5JP-PRO-LYS-ARG-ILE.1 Ligand excluded by PLIP UNX.41: 2 residues within 4Å: Chain A: Q.212 Ligands: 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
A

Alpha N-terminal protein methyltransferase 1B

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