SMTL ID : 4ij8.1

Crystal structure of the complex of SETD8 with SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 16 residues within 4Å: Chain A: G.38, K.39, G.40, R.41, C.83, Y.84, R.108, L.109, I.110, N.111, H.112, Y.149, W.162 Chain B: A.159 Ligands: UNX.7, UNX.16 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.41, A:Y.84, A:N.111, A:N.111, A:H.112, A:H.112 Salt bridges: A:R.41 pi-Stacking: A:W.162, A:W.162, A:W.162 pi-Cation interactions: A:Y.84 SAM.15: 14 residues within 4Å: Chain A: A.159 Chain B: G.38, K.39, R.41, C.83, Y.84, R.108, L.109, I.110, N.111, H.112, Y.149, W.162 Ligands: UNX.23 14 PLIP interactions: 1 interactions with chain A, 13 interactions with chain B Water bridges: A:H.160, B:K.39 Hydrogen bonds: B:R.41, B:R.41, B:Y.84, B:N.111, B:N.111, B:H.112, B:H.112 Salt bridges: B:R.41 pi-Stacking: B:W.162, B:W.162, B:W.162 pi-Cation interactions: B:Y.84

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

UNX.2: 2 residues within 4Å: Chain A: G.82, M.85 Ligand excluded by PLIP UNX.3: 2 residues within 4Å: Chain A: D.53, F.54 Ligand excluded by PLIP UNX.4: 1 residues within 4Å: Chain A: T.120 Ligand excluded by PLIP UNX.5: 1 residues within 4Å: Chain A: D.37 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: D.37, G.38 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: G.38 Ligands: SAM.1, UNX.23 Ligand excluded by PLIP UNX.8: 1 residues within 4Å: Chain A: Y.87 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: Y.90, L.91 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: M.85, D.98, T.100 Chain B: Q.77 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: Y.86, G.150, D.151 Ligand excluded by PLIP UNX.12: 4 residues within 4Å: Chain A: Y.58, C.83, Y.147, Y.149 Ligand excluded by PLIP UNX.13: 1 residues within 4Å: Chain A: Y.75 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: S.7, K.8, A.9 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain B: H.160 Ligands: SAM.1 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain B: Y.86, Y.87 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain B: G.82, M.85 Ligand excluded by PLIP UNX.19: 1 residues within 4Å: Chain B: T.120 Ligand excluded by PLIP UNX.20: 1 residues within 4Å: Chain B: L.62 Ligand excluded by PLIP UNX.21: 1 residues within 4Å: Chain B: T.103 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain B: Y.58, C.83, Y.147, Y.149 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain B: G.38 Ligands: UNX.7, SAM.15 Ligand excluded by PLIP UNX.24: 3 residues within 4Å: Chain B: I.19, D.53, F.54 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, W. et al., Crystal structure of the complex of SETD8 with SAM. To be Published

Release Date

2013-01-16

Peptides

N-lysine methyltransferase SETD8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-lysine methyltransferase SETD8