SMTL ID : 5v9i.1 (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.11: 6 residues within 4Å: Chain B: C.64, C.77, C.107, C.111 Ligands: ZN.12, ZN.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.77, B:C.107, B:C.111 ZN.12: 6 residues within 4Å: Chain B: C.70, C.107, C.113, C.117 Ligands: ZN.11, ZN.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:C.107, B:C.113, B:C.117 ZN.13: 6 residues within 4Å: Chain B: C.64, C.66, C.70, C.75 Ligands: ZN.11, ZN.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.66, B:C.70, B:C.75 ZN.14: 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 Ligands: UNX.10 11 PLIP interactions: 11 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:R.134, A:S.174, A:Y.175 SAM.15: 17 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, F.256, T.257, C.258, Q.259 Ligands: UNX.21 12 PLIP interactions: 12 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:Q.259, B:C.260 Water bridges: B:R.134, B:S.174, B:Y.175

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: 12 residues within 4Å: Chain A: D.164, A.167, D.168, R.170, D.173, L.176, D.178, C.188, R.247, F.248, K.252 Ligands: GOL.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.176, A:L.176 Hydrogen bonds: A:D.173, A:D.173 Water bridges: A:F.248 Salt bridges: A:D.168 90P.16: 11 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, K.252 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.164, B:A.167, B:L.176, B:L.176 Hydrogen bonds: B:D.173 Water bridges: B:F.248

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: E.21, V.122, G.125, I.126, F.153, C.155, E.156, N.196 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.126, A:E.156, A:E.156, A:E.156, A:N.196 Water bridges: A:N.22, A:R.225 GOL.8: 4 residues within 4Å: Chain A: I.11, P.26, V.28, Q.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.131 GOL.9: 7 residues within 4Å: Chain A: L.176, F.177, D.178, F.242, D.243, Y.244 Ligands: 90P.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.178, A:D.178, A:D.243 Water bridges: A:Y.157, A:L.176, A:D.178 GOL.17: 7 residues within 4Å: Chain B: V.122, G.125, I.126, F.153, C.155, E.156, N.196 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.122, B:E.156, B:E.156, B:N.196, B:R.225 Water bridges: B:I.126 GOL.18: 8 residues within 4Å: Chain B: V.31, D.32, R.134, T.135, A.136, K.137, M.138, G.139 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.135, B:G.139, B:G.139 Water bridges: B:V.31 GOL.19: 6 residues within 4Å: Chain B: N.46, L.161, H.218, F.223, P.224, R.225 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.46, B:F.223, B:P.224 Water bridges: B:N.46, B:N.46, B:R.225, B:R.225, B:R.225

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

UNX.10: 3 residues within 4Å: Chain A: D.39, Y.175 Ligands: SAM.5 No protein-ligand interaction detected (PLIP) UNX.20: 5 residues within 4Å: Chain B: S.81, C.84, I.104, F.105, N.119 No protein-ligand interaction detected (PLIP) UNX.21: 3 residues within 4Å: Chain B: W.140, Y.175 Ligands: SAM.15 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
A

B
B

Histone-lysine N-methyltransferase EHMT2

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