SMTL ID : 3rq4.1

Crystal structure of suppressor of variegation 4-20 homolog 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.184, C.228, C.230, C.233 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.184, A:C.228, A:C.230, A:C.233

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 19 residues within 4Å: Chain A: H.31, Y.113, M.115, E.116, G.119, A.120, F.159, S.160, A.178, F.179, I.180, N.181, H.182, Y.216, F.221, C.228, E.229, C.230 Ligands: EDO.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.116, A:A.120, A:F.159, A:N.181, A:H.182, A:H.182, A:E.229 Water bridges: A:H.31, A:Y.113 Salt bridges: A:H.31 pi-Stacking: A:Y.113, A:Y.113, A:F.221

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: D.158, F.159, S.160, I.161, Y.216, F.220 Ligands: SAM.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.161, A:I.161

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

UNX.4: 1 residues within 4Å: Chain A: Y.76 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: T.125, R.126 Ligand excluded by PLIP UNX.6: 1 residues within 4Å: Chain A: R.112 Ligand excluded by PLIP UNX.7: 1 residues within 4Å: Chain A: R.112 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: C.110, K.121 Ligands: UNX.9, UNX.14 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: K.121 Ligands: UNX.8 Ligand excluded by PLIP UNX.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: L.152, R.153, A.154 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: V.191, P.192 Ligand excluded by PLIP UNX.13: 2 residues within 4Å: Chain A: H.231, E.234 Ligand excluded by PLIP UNX.14: 5 residues within 4Å: Chain A: P.109, C.110, T.111, K.121 Ligands: UNX.8 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: C.184, P.186 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: R.29, T.30 Ligand excluded by PLIP UNX.17: 1 residues within 4Å: Chain A: L.136 Ligand excluded by PLIP UNX.18: 5 residues within 4Å: Chain A: P.192, A.193, D.194, G.195, A.197 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: N.131, K.189, K.201 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain A: G.70, R.75 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: R.204, D.205 Ligand excluded by PLIP UNX.22: 5 residues within 4Å: Chain A: N.187, R.204, D.205, I.206, D.210 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Chain A: R.58, D.59 Ligand excluded by PLIP UNX.24: 3 residues within 4Å: Chain A: A.154, E.156 Ligands: UNX.31 Ligand excluded by PLIP UNX.25: 3 residues within 4Å: Chain A: G.81, P.82, R.83 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain A: G.219, F.220, F.221, G.222 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain A: E.116, T.117 Ligand excluded by PLIP UNX.28: 1 residues within 4Å: Chain A: T.165 Ligand excluded by PLIP UNX.29: 1 residues within 4Å: Chain A: E.52 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain A: Q.78, R.80, G.81 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain A: G.155, E.156 Ligands: UNX.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, H. et al., Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2. Febs Lett. (2013)

Release Date

2011-06-01

Peptides

Histone-lysine N-methyltransferase SUV420H2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SUV420H2