SMTL ID : 5e2b.1 (1 other biounit)

Crystal structure of NTMT1 in complex with N-terminally methylated PPKRIA peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x 3BY- PRO- LYS- ARG- ILE- ALA: RCC1(Non-covalent)

3BY-PRO-LYS-ARG-ILE-ALA.1: 15 residues within 4Å: Chain A: W.38, M.48, L.49, G.50, Y.52, I.55, W.154, N.186, D.195, D.198, S.200, E.231, I.232, Y.233 Ligands: SAH.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.52, A:I.55, A:W.154, A:I.232, A:Y.233, A:Y.233 Hydrogen bonds: A:N.186, A:D.195, A:D.195, A:S.200, A:E.231, A:Y.233, A:Y.233 Water bridges: A:N.186, A:Y.233 Salt bridges: A:E.231

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

SAH.2: 21 residues within 4Å: Chain A: W.38, M.48, G.87, A.88, G.89, R.92, I.93, D.109, I.110, T.111, F.114, C.135, G.136, L.137, Q.138, Q.153, W.154, V.155, H.158, L.159 Ligands: 3BY-PRO-LYS-ARG-ILE-ALA.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.87, A:I.110, A:T.111, A:T.111, A:T.111, A:L.137, A:Q.138 Water bridges: A:A.88, A:Q.153 Salt bridges: A:R.92

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: H.54, I.55, I.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.54, A:H.54 GOL.4: 2 residues within 4Å: Chain A: E.104, R.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.104, A:R.130

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

UNX.5: 1 residues within 4Å: Chain A: Q.40 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: L.71, K.77, T.78, T.80 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: L.101, F.102, R.103 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: E.27 Ligands: UNX.16 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: Q.138, R.170 Ligands: UNX.28 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain A: V.45, Y.121 Ligand excluded by PLIP UNX.11: 4 residues within 4Å: Chain A: E.143, P.144, D.145, S.146 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: Q.189, H.234 Ligands: UNX.24 Ligand excluded by PLIP UNX.13: 2 residues within 4Å: Chain A: S.21, E.22 Ligand excluded by PLIP UNX.14: 6 residues within 4Å: Chain A: W.154, V.155, I.156, G.157, D.185 Ligands: UNX.31 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: K.127, V.129, R.130 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: E.27, H.163 Ligands: UNX.8 Ligand excluded by PLIP UNX.17: 4 residues within 4Å: Chain A: F.70, N.76, T.78, N.178 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: R.130, E.143 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: C.213, G.216, L.217 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain A: K.35, I.110, T.111, E.112 Ligands: UNX.27 Ligand excluded by PLIP UNX.21: 1 residues within 4Å: Chain A: L.194 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain A: K.95, R.96 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain A: T.20, T.160, D.161, Q.162 Ligand excluded by PLIP UNX.24: 3 residues within 4Å: Chain A: H.234, Y.236 Ligands: UNX.12 Ligand excluded by PLIP UNX.25: 1 residues within 4Å: Chain A: I.41 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain A: Q.138, D.139 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain A: K.39, T.111 Ligands: UNX.20 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain A: Q.138, H.163 Ligands: UNX.9 Ligand excluded by PLIP UNX.29: 5 residues within 4Å: Chain A: G.74, P.75, K.77, N.178 Ligands: UNX.30 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain A: P.75, N.178 Ligands: UNX.29 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain A: S.200 Ligands: UNX.14 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., Structural basis for substrate recognition by the human N-terminal methyltransferase 1. Genes Dev. (2015)

Release Date

2015-10-28

Peptides

N-terminal Xaa-Pro-Lys N-methyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-terminal Xaa-Pro-Lys N-methyltransferase 1

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