SMTL ID : 5v9j.1

Crystal structure of catalytic domain of GLP with MS0105

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

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

SAM.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 Ligands: UNX.15 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:W.159, A:S.193, A:Y.194, A:Y.194, A:N.221, A:N.221, A:H.222, A:H.222, A:R.278 Water bridges: A:R.278, A:R.278, A:R.278 SAM.16: 17 residues within 4Å: Chain B: 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 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:W.159, B:S.193, B:Y.194, B:Y.194, B:N.221, B:N.221, B:H.222, B:H.222, B:R.278 Water bridges: B:S.193

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

90P.2: 14 residues within 4Å: Chain A: D.183, A.186, D.187, R.189, D.192, L.195, D.197, V.205, C.207, Y.263, R.266, F.267, I.270, K.271 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.183, A:L.195, A:L.195, A:V.205, A:I.270 Hydrogen bonds: A:D.192, A:D.192 Salt bridges: A:D.192 90P.17: 14 residues within 4Å: Chain B: D.183, A.186, D.187, R.189, D.192, L.195, D.197, V.205, C.207, Y.263, R.266, F.267, I.270, K.271 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.183, B:L.195, B:L.195, B:V.205, B:I.270 Hydrogen bonds: B:D.192, B:D.192

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: C.83, C.96, C.126, C.130 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.96, A:C.126, A:C.130 ZN.4: 7 residues within 4Å: Chain A: C.83, C.89, C.126, C.132, C.136 Ligands: ZN.3, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.89, A:C.126, A:C.132, A:C.136 ZN.5: 6 residues within 4Å: Chain A: C.83, C.85, C.89, C.94 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.85, A:C.89, A:C.94 ZN.6: 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.18: 6 residues within 4Å: Chain B: C.83, C.96, C.126, C.130 Ligands: ZN.19, ZN.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:C.96, B:C.126, B:C.130 ZN.19: 7 residues within 4Å: Chain B: C.83, C.89, C.126, C.132, C.136 Ligands: ZN.18, ZN.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.89, B:C.126, B:C.132, B:C.136 ZN.20: 6 residues within 4Å: Chain B: C.83, C.85, C.89, C.94 Ligands: ZN.18, ZN.19 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:C.85, B:C.89, B:C.94 ZN.21: 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

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: R.139, V.140, N.143, R.146 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: R.75, H.237 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: R.75, H.237 Ligand excluded by PLIP

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

UNX.9: 3 residues within 4Å: Chain A: D.156, M.157, G.158 No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain A: L.80, Q.81 No protein-ligand interaction detected (PLIP) UNX.11: 3 residues within 4Å: Chain A: L.111, L.112, G.170 No protein-ligand interaction detected (PLIP) UNX.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.13: 3 residues within 4Å: Chain A: P.56, S.57, N.58 No protein-ligand interaction detected (PLIP) UNX.14: 1 residues within 4Å: Chain A: N.65 No protein-ligand interaction detected (PLIP) UNX.15: 2 residues within 4Å: Chain A: S.193 Ligands: SAM.1 No protein-ligand interaction detected (PLIP) UNX.24: 3 residues within 4Å: Chain A: R.33 Chain B: W.133, N.135 No protein-ligand interaction detected (PLIP) UNX.25: 3 residues within 4Å: Chain B: D.108, G.109, R.146 No protein-ligand interaction detected (PLIP) UNX.26: 5 residues within 4Å: Chain B: T.154, R.155, D.156, M.157, G.158 No protein-ligand interaction detected (PLIP) UNX.27: 2 residues within 4Å: Chain B: E.191, R.211 No protein-ligand interaction detected (PLIP) UNX.28: 1 residues within 4Å: Chain B: R.75 No protein-ligand interaction detected (PLIP) UNX.29: 4 residues within 4Å: Chain B: V.67, P.70, M.71, N.72 No protein-ligand interaction detected (PLIP)

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.23: 5 residues within 4Å: Chain B: C.85, I.86, D.87, S.91, N.93 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.86, B:D.87 Salt bridges: B:D.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2018-03-21

Peptides

Histone-lysine N-methyltransferase EHMT1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase EHMT1

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