SMTL ID : 6kdr.1

Crystal structure of human NRMT2 in complex with human centromere protein B peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

2 x GLY- PRO- LYS- ARG- ARG- GLN: Peptide from Major centromere autoantigen B(Non-covalent)

GLY-PRO-LYS-ARG-ARG-GLN.1: 19 residues within 4Å: Chain A: M.47, M.48, F.51, L.54, W.152, N.184, A.186, R.187, I.191, D.193, D.196, S.198, Q.229, C.230, I.231, P.232 Chain B: V.22, N.24 Ligands: GOL.4 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.51, A:F.51, A:L.54, A:W.152, A:I.191, A:I.231 Hydrogen bonds: A:M.47, A:N.184, A:R.187, A:R.187, A:R.187, A:D.193, A:S.198, A:Q.229, A:Q.229, A:I.231, B:N.24, B:N.24 Water bridges: A:N.184 GLY-PRO-LYS-ARG-ARG-GLN.2: 16 residues within 4Å: Chain A: N.24, K.212 Chain B: M.48, F.51, W.152, N.184, E.188, D.193, D.196, S.198, E.228, Q.229, C.230, I.231 Ligands: GOL.7, CL.10 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:N.24, B:N.184, B:D.193, B:D.196, B:S.198, B:Q.229, B:I.231 Hydrophobic interactions: B:F.51, B:W.152, B:I.231 Water bridges: B:Y.37, B:N.184

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

SAH.3: 20 residues within 4Å: Chain A: Y.37, M.47, G.85, S.86, G.87, R.90, V.91, D.107, M.108, M.109, F.112, Y.133, S.134, L.135, Q.136, Q.151, W.152, V.153, H.156, L.157 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.85, A:G.87, A:M.108, A:L.135, A:Q.136 Water bridges: A:G.89, A:S.134, A:Q.151 Salt bridges: A:R.90 SAH.6: 20 residues within 4Å: Chain B: Y.37, M.47, G.85, S.86, G.87, R.90, V.91, D.107, M.108, M.109, F.112, Y.133, S.134, L.135, Q.136, Q.151, W.152, V.153, H.156, L.157 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.85, B:M.108, B:L.135, B:Q.136 Water bridges: B:S.86, B:R.90, B:S.134, B:Q.151 Salt bridges: B:R.90

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: W.152, V.153, G.155, H.156, D.183, D.196, S.198 Ligands: GLY-PRO-LYS-ARG-ARG-GLN.1, GLY-PRO-LYS-ARG-ARG-GLN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.155, A:D.183, A:S.198 Water bridges: A:Y.37, A:H.156, A:N.184, A:N.184 GOL.7: 10 residues within 4Å: Chain B: W.152, V.153, S.154, G.155, H.156, D.183, D.196, S.198 Ligands: GLY-PRO-LYS-ARG-ARG-GLN-LEU-THR-PHE.2, GLY-PRO-LYS-ARG-ARG-GLN-LEU-THR-PHE.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.152, B:G.155, B:D.183, B:D.196 Water bridges: B:D.196 GOL.8: 6 residues within 4Å: Chain B: L.173, K.174, E.175, N.176, G.177, H.239 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.176, B:G.177 Water bridges: B:R.170, B:L.173

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

CL.5: 2 residues within 4Å: Chain A: R.207, V.217 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: A.186, R.187, I.231, P.232 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Ligands: GLY-PRO-LYS-ARG-ARG-GLN-LEU-THR-PHE.2, GLY-PRO-LYS-ARG-ARG-GLN-LEU-THR-PHE.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., Substrate-enzyme engagement regulates state-specific alpha-N methylation of NRMT2. to be published

Release Date

2020-07-08

Peptides

Alpha N-terminal protein methyltransferase 1B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha N-terminal protein methyltransferase 1B

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