SMTL ID : 2rfi.3 (2 other biounits)

Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

hetero-2-2-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.81, C.94, C.124, C.128 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.81, A:C.94, A:C.124, A:C.128 ZN.2: 6 residues within 4Å: Chain A: C.87, C.124, C.130, C.134 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.87, A:C.124, A:C.130, A:C.134 ZN.3: 6 residues within 4Å: Chain A: C.81, C.83, C.87, C.92 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.81, A:C.83, A:C.87, A:C.92 ZN.4: 4 residues within 4Å: Chain A: C.222, C.275, C.277, C.282 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.222, A:C.275, A:C.277, A:C.282 ZN.7: 6 residues within 4Å: Chain B: C.81, C.94, C.124, C.128 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.81, B:C.94, B:C.124, B:C.128 ZN.8: 6 residues within 4Å: Chain B: C.87, C.124, C.130, C.134 Ligands: ZN.7, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.87, B:C.124, B:C.130, B:C.134 ZN.9: 6 residues within 4Å: Chain B: C.81, C.83, C.87, C.92 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.81, B:C.83, B:C.87, B:C.92 ZN.10: 4 residues within 4Å: Chain B: C.222, C.275, C.277, C.282 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.222, B:C.275, B:C.277, B:C.282

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

SAH.5: 17 residues within 4Å: Chain A: M.155, G.156, W.157, S.191, Y.192, R.216, F.217, N.219, H.220, Y.261, F.265, F.273, S.274, C.275, R.276, C.277 Chain C: K.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.157, A:W.157, A:W.157, A:S.191, A:N.219, A:H.220, A:H.220, A:R.276 Water bridges: A:Y.192, A:R.276 SAH.6: 15 residues within 4Å: Chain B: M.155, G.156, W.157, S.191, Y.192, R.216, F.217, N.219, H.220, Y.261, F.273, S.274, C.275, R.276 Chain D: K.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:M.155, B:W.157, B:W.157, B:S.191, B:S.191, B:Y.192, B:N.219, B:H.220, B:H.220, B:H.220, B:R.276, B:R.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, H. et al., Structural biology of human H3K9 methyltransferases. Plos One (2010)

Release Date

2007-10-23

Peptides

Histone-lysine N-methyltransferase, H3 lysine-9 specific 5: AB
Histone H3: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
P

D
Q

Histone-lysine N-methyltransferase, H3 lysine-9 specific 5

Histone H3

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