SMTL ID : 5v9i.2 (1 other biounit)

Crystal structure of catalytic domain of G9a with MS0105

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.64, C.77, C.107, C.111 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.77, A:C.107, A:C.111 ZN.2: 5 residues within 4Å: Chain A: C.70, C.107, C.113, C.117 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.70, A:C.107, A:C.113, A:C.117 ZN.3: 7 residues within 4Å: Chain A: C.64, C.66, C.70, C.75, C.107 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.66, A:C.70, A:C.75 ZN.4: 4 residues within 4Å: Chain A: C.205, C.258, C.260, C.265 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.205, A:C.258, A:C.260, A:C.265 ZN.9: 6 residues within 4Å: Chain B: C.64, C.77, C.107, C.111 Ligands: ZN.10, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.77, B:C.107, B:C.111 ZN.10: 6 residues within 4Å: Chain B: C.70, C.107, C.113, C.117 Ligands: ZN.9, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:C.107, B:C.113, B:C.117 ZN.11: 6 residues within 4Å: Chain B: C.64, C.66, C.70, C.75 Ligands: ZN.9, ZN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.66, B:C.70, B:C.75 ZN.12: 4 residues within 4Å: Chain B: C.205, C.258, C.260, C.265 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.205, B:C.258, B:C.260, B:C.265

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

SAM.5: 17 residues within 4Å: Chain A: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, I.201, N.202, H.203, Y.244, F.248, F.256, T.257, C.258, Q.259, C.260 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.140, A:S.174, A:Y.175, A:N.202, A:N.202, A:H.203, A:H.203, A:Q.259 Water bridges: A:S.174, A:Y.175 SAM.13: 18 residues within 4Å: Chain B: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, I.201, N.202, H.203, Y.244, F.248, W.249, F.256, T.257, C.258, Q.259, C.260 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:W.140, B:S.174, B:Y.175, B:N.202, B:N.202, B:H.203, B:H.203, B:Y.244, B:Q.259 Water bridges: B:S.174, B:Q.259

2 x 90P: N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine(Non-covalent)

90P.6: 13 residues within 4Å: Chain A: D.164, A.167, D.168, R.170, D.173, L.176, D.178, C.188, Y.244, R.247, F.248, I.251, K.252 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.176, A:L.176, A:I.251 Hydrogen bonds: A:D.173, A:D.173 Water bridges: A:F.248 Salt bridges: A:D.168 90P.14: 12 residues within 4Å: Chain B: D.164, A.167, D.168, R.170, D.173, L.176, D.178, C.188, R.247, F.248, I.251, K.252 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.164, B:L.176, B:I.251 Hydrogen bonds: B:D.173 Salt bridges: B:D.168

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: V.122, G.125, I.126, F.153, C.155, E.156, N.196, R.225 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.122, A:I.126, A:E.156, A:E.156, A:N.196, A:R.225 GOL.15: 7 residues within 4Å: Chain A: W.114 Chain B: D.15, G.19, E.21, N.22, V.23, P.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.15, B:E.21 Water bridges: B:G.19 GOL.16: 7 residues within 4Å: Chain B: V.31, D.32, T.135, A.136, K.137, M.138, G.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.135, B:M.138, B:G.139

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

UNX.8: 1 residues within 4Å: Chain A: P.26 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, H. et al., Crystal structure of catalytic domain of G9a with MS0105. to be published

Release Date

2018-03-21

Peptides

Histone-lysine N-methyltransferase EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Histone-lysine N-methyltransferase EHMT2

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