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

Crystal structure of Toxoplasma gondii AKMT

Coordinates

PDB Format Compare

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.12: 4 residues within 4Å: Chain B: C.158, C.214, C.216, C.219 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.158, B:C.214, B:C.216, B:C.219 ZN.13: 4 residues within 4Å: Chain B: C.231, C.234, C.253, C.256 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.231, B:C.234, B:C.253, B:C.256

3 x SO4: SULFATE ION

SO4.3: 6 residues within 4Å: Chain A: N.384, S.387, R.388, E.391, E.419 Chain B: N.295 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.388, A:E.391, A:E.419, B:N.295 SO4.14: 6 residues within 4Å: Chain A: N.302 Chain B: N.377, S.380, R.381, E.384, E.412 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.377, B:S.380, B:S.380, A:N.302 Water bridges: B:E.384, A:T.305 SO4.15: 5 residues within 4Å: Chain A: L.240, C.241 Chain B: Y.387, N.388, Y.391 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.388

4 x GOL: GLYCEROL

GOL.4: 8 residues within 4Å: Chain A: T.207, R.210, R.225, D.231, N.232, A.233, V.348 Ligands: GOL.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.166, A:T.207, A:T.207, A:R.210, A:R.210, A:R.225, A:N.232 GOL.5: 8 residues within 4Å: Chain A: R.237, Y.301, T.305, F.308, L.314, H.318 Chain B: R.381 Ligands: EDO.17 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.237, A:Y.301, A:Y.301, A:F.308 Water bridges: B:H.382 GOL.6: 6 residues within 4Å: Chain A: Y.360, D.392 Chain B: R.230, T.236, A.302, K.336 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.360, A:D.392, B:R.230, B:R.230, B:A.302 GOL.7: 4 residues within 4Å: Chain A: R.166, V.224, A.228 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.166, A:R.166

11 x EDO: 1,2-ETHANEDIOL

EDO.8: 2 residues within 4Å: Chain A: R.285, Q.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.285 EDO.9: 5 residues within 4Å: Chain A: Q.338, R.341, W.358, L.359, E.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.338, A:R.341, A:R.341, A:W.358 EDO.10: 3 residues within 4Å: Chain A: N.395, Y.398 Chain B: L.233 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.232 EDO.11: 6 residues within 4Å: Chain A: A.167, A.169, R.184, S.196, D.200, L.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.200 Water bridges: A:S.164, A:A.167 EDO.16: 4 residues within 4Å: Chain B: C.24, A.155, H.156, E.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.156, B:E.185 Water bridges: B:S.157 EDO.17: 6 residues within 4Å: Chain A: R.237, T.243, K.343 Chain B: Y.353, D.385 Ligands: GOL.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.385, A:R.237, A:R.237 Water bridges: B:D.385 EDO.18: 5 residues within 4Å: Chain B: R.177, D.193, L.196, S.346, Y.347 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.347 Water bridges: B:R.177 EDO.19: 3 residues within 4Å: Chain B: R.132, Y.133, W.210 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.132, B:R.132 EDO.20: 6 residues within 4Å: Chain A: P.350 Chain B: A.252, C.253, T.254, Q.257 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.253 EDO.21: 5 residues within 4Å: Chain B: F.240, S.251, A.252, T.254 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.252 EDO.22: 2 residues within 4Å: Chain B: Y.268, R.299 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.299

1 x PEG: DI(HYDROXYETHYL)ETHER

PEG.23: 4 residues within 4Å: Chain B: A.274, Y.275, L.292, Q.296 No protein-ligand interaction detected (PLIP)

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
A

B
B

Apical complex lysine methyltransferase

Apical complex lysine methyltransferase