SMTL ID : 6fnd.2 (1 other biounit)

Crystal structure of Toxoplasma gondii AKMT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

4 x ZN: ZINC ION

ZN.1: 4 residues within 4Å: Chain A: C.165, C.221, C.223, C.226 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.165, A:C.221, A:C.223, A:C.226 ZN.2: 4 residues within 4Å: Chain A: C.238, C.241, C.260, C.263 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:C.241, A:C.260, A:C.263 ZN.13: 4 residues within 4Å: Chain B: C.165, C.221, C.223, C.226 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.165, B:C.221, B:C.223, B:C.226 ZN.14: 4 residues within 4Å: Chain B: C.238, C.241, C.260, C.263 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.238, B:C.241, B:C.260, B:C.263

2 x SO4: SULFATE ION

SO4.3: 1 residues within 4Å: Chain A: I.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.43 SO4.15: 6 residues within 4Å: Chain A: N.302 Chain B: N.384, S.387, R.388, E.391, E.419 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:N.302, B:N.384, B:N.384, B:S.387, B:R.388, B:E.419 Water bridges: A:T.305, B:R.388, B:R.388

4 x GOL: GLYCEROL

GOL.4: 7 residues within 4Å: Chain A: T.207, R.210, R.225, D.231, N.232, A.233, V.348 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.207, A:T.207, A:T.207, A:R.210, A:R.210, A:R.225, A:N.232, A:V.348 Water bridges: A:N.232, A:N.232 GOL.5: 7 residues within 4Å: Chain A: R.237, T.243, A.309 Chain B: Y.360, D.392 Ligands: EDO.9, EDO.10 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.237, A:R.237, A:A.309, B:Y.360, B:D.392 GOL.16: 8 residues within 4Å: Chain B: T.207, R.210, R.225, V.230, D.231, N.232, A.233, V.348 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.207, B:R.210, B:R.210, B:R.225, B:D.231 GOL.17: 4 residues within 4Å: Chain B: F.247, S.258, A.259, T.261 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.259

10 x EDO: 1,2-ETHANEDIOL

EDO.6: 5 residues within 4Å: Chain A: C.31, A.162, H.163, E.192, C.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.163 Water bridges: A:V.224 EDO.7: 6 residues within 4Å: Chain A: N.384, S.387, R.388, E.391, E.419 Chain B: N.302 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.302, A:R.388, A:E.391 Water bridges: A:R.388 EDO.8: 4 residues within 4Å: Chain A: Y.360, D.392 Chain B: R.237, A.309 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.237, B:R.237, A:D.392 EDO.9: 5 residues within 4Å: Chain A: Y.301, L.314 Chain B: R.388 Ligands: GOL.5, EDO.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.237 Water bridges: A:Y.301, B:R.388, B:H.389 EDO.10: 8 residues within 4Å: Chain A: F.336, E.340, K.343 Chain B: M.339, Y.360, H.389 Ligands: GOL.5, EDO.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.392, A:E.340 EDO.11: 3 residues within 4Å: Chain A: R.139, Y.140, W.217 No protein-ligand interaction detected (PLIP) EDO.12: 2 residues within 4Å: Chain A: D.200, Y.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.200 EDO.18: 3 residues within 4Å: Chain B: A.281, R.285, Q.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.285 EDO.19: 5 residues within 4Å: Chain B: C.31, A.162, H.163, E.192, T.194 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.164, B:S.164, B:S.164 EDO.20: 3 residues within 4Å: Chain B: K.28, F.143, Y.197 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.200, B:D.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pivovarova, Y. et al., Structure of a Novel Dimeric SET Domain Methyltransferase that Regulates Cell Motility. J. Mol. Biol. (2018)

Release Date

2018-11-14

Peptides

Apical complex lysine methyltransferase: A
Apical complex lysine methyltransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Apical complex lysine methyltransferase

Apical complex lysine methyltransferase