SMTL ID : 7wew.1

Structure of adenylation domain of epsilon-poly-L-lysine synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: A.380, A.381, R.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.381, A:R.382 Water bridges: A:G.356 SO4.2: 2 residues within 4Å: Chain A: R.468, Q.472 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.472 Water bridges: A:R.468, A:Q.472 Salt bridges: A:R.468 SO4.3: 3 residues within 4Å: Chain A: G.411, R.412, R.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.413 Salt bridges: A:R.412, A:R.413 SO4.4: 4 residues within 4Å: Chain A: D.404, D.405, Q.406, R.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.405, A:Q.406 Salt bridges: A:R.413 SO4.5: 2 residues within 4Å: Chain A: D.196, R.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.196 Salt bridges: A:R.316 SO4.6: 1 residues within 4Å: Chain A: R.180 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.357 Salt bridges: A:R.180

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: P.260, T.261, E.282, S.283, P.285, D.420, A.432, A.433, V.497, R.499 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.283 Water bridges: A:S.283, A:D.420, A:A.432 GOL.8: 6 residues within 4Å: Chain A: S.283, F.399, V.400, G.417, E.418, A.421 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.283, A:F.399, A:G.417 GOL.9: 5 residues within 4Å: Chain A: R.239, A.240, G.241, H.242, E.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.240, A:G.241, A:H.242, A:E.243

1 x LAD: ADENOSINE-5'-[LYSYL-PHOSPHATE](Non-covalent)

LAD.10: 24 residues within 4Å: Chain A: T.165, F.213, D.214, A.215, E.218, S.257, I.278, V.279, G.280, G.281, E.282, S.283, N.301, T.302, Y.303, G.304, P.305, T.306, V.310, V.311, I.325, D.388, F.399, K.496 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.213, A:A.215 Hydrogen bonds: A:T.165, A:T.165, A:D.214, A:G.281, A:N.301, A:T.302, A:T.302, A:T.302, A:Y.303, A:G.304, A:T.306, A:T.306, A:K.496 Water bridges: A:G.280, A:C.284, A:T.386, A:D.388, A:D.388 Salt bridges: A:K.496, A:K.496

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okamoto, T. et al., Crystal structure of the adenylation domain from an epsilon-poly-l-lysine synthetase provides molecular mechanism for substrate specificity. Biochem.Biophys.Res.Commun. (2022)

Release Date

2022-02-09

Peptides

Epsilon-poly-L-lysine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Epsilon-poly-L-lysine synthase