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

Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

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

SAH.1: 18 residues within 4Å: Chain A: M.157, G.158, W.159, S.193, Y.194, R.218, F.219, I.220, N.221, H.222, Y.263, F.267, F.275, S.276, C.277, R.278, C.279 Chain C: K.9 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:W.159, A:W.159, A:W.159, A:S.193, A:N.221, A:H.222, A:H.222, A:R.278 Water bridges: A:S.193, A:Y.194, A:R.278 SAH.6: 17 residues within 4Å: Chain B: M.157, G.158, W.159, S.193, Y.194, R.218, F.219, N.221, H.222, Y.263, F.267, F.275, S.276, C.277, R.278, C.279 Chain D: K.9 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:W.159, B:W.159, B:W.159, B:S.193, B:Y.194, B:N.221, B:H.222, B:H.222, B:H.222, B:R.278 Water bridges: B:S.193, B:R.278

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.83, C.96, C.126, C.130 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.96, A:C.126, A:C.130 ZN.3: 7 residues within 4Å: Chain A: C.83, C.89, C.126, C.132, C.136 Ligands: ZN.2, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.89, A:C.126, A:C.132, A:C.136 ZN.4: 6 residues within 4Å: Chain A: C.83, C.85, C.89, C.94 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.85, A:C.89, A:C.94 ZN.5: 4 residues within 4Å: Chain A: C.224, C.277, C.279, C.284 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.224, A:C.277, A:C.279, A:C.284 ZN.7: 6 residues within 4Å: Chain B: C.83, C.96, C.126, C.130 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:C.96, B:C.126, B:C.130 ZN.8: 6 residues within 4Å: Chain B: C.89, C.126, C.132, C.136 Ligands: ZN.7, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.89, B:C.126, B:C.132, B:C.136 ZN.9: 6 residues within 4Å: Chain B: C.83, C.85, C.89, C.94 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:C.85, B:C.89, B:C.94 ZN.10: 4 residues within 4Å: Chain B: C.224, C.277, C.279, C.284 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.224, B:C.277, B:C.279, B:C.284

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

2009-06-09

Peptides

Histone-lysine N-methyltransferase, H3 lysine-9 specific 5: AB
Mono-Methylated H3K9 Peptide: 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

Mono-Methylated H3K9 Peptide

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