SMTL ID : 2cdq.1

Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

4 x LYS: LYSINE(Non-covalent)

LYS.1: 10 residues within 4Å: Chain A: S.371, V.372, D.373 Chain B: M.351, Q.354, V.355, G.356, F.357, L.358, S.378 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.356, B:F.357, B:L.358, B:S.378, A:V.372, A:V.372 Water bridges: A:D.373 LYS.2: 7 residues within 4Å: Chain A: G.35, S.64, A.65, T.70, E.148, G.232, S.233 8 PLIP interactions: 8 interactions with chain A, Hydrogen bonds: A:G.35, A:S.64, A:A.65, A:E.148, A:E.148 Water bridges: A:K.68, A:G.231, A:D.234 LYS.5: 10 residues within 4Å: Chain A: M.351, Q.354, V.355, G.356, F.357, L.358, S.378 Chain B: S.371, V.372, D.373 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.351, A:L.358 Hydrogen bonds: A:G.356, A:F.357, A:L.358, A:S.378, B:V.372, B:V.372 LYS.6: 7 residues within 4Å: Chain B: S.64, A.65, T.70, E.148, F.215, G.232, S.233 13 PLIP interactions: 11 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:T.70, B:F.215 Hydrogen bonds: B:G.35, B:S.64, B:S.64, B:S.64, B:A.65, B:G.232, B:S.233, B:S.233, B:S.233 Water bridges: K.6, K.6

2 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.3: 6 residues within 4Å: Chain A: R.297 Chain B: S.348, T.349, R.350, I.411, A.412 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.349, B:T.349, B:T.349, B:R.350, B:R.350, B:R.350, B:V.413 Salt bridges: A:R.297 TAR.7: 8 residues within 4Å: Chain A: A.347, S.348, T.349, R.350, I.411, A.412, V.413 Chain B: R.297 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.348, A:T.349, A:R.350, A:R.350, A:R.350, A:V.413 Water bridges: A:S.348, A:R.350 Salt bridges: B:R.297

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

SAM.4: 10 residues within 4Å: Chain A: L.368, G.369, I.370, S.371, D.387, W.392, S.393, R.394, L.396, E.400 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.371, A:S.371, A:D.387, A:S.393, A:S.393, A:R.394, A:R.394 Salt bridges: A:E.400 pi-Stacking: A:W.392, A:W.392, A:W.392 SAM.8: 10 residues within 4Å: Chain B: L.368, G.369, I.370, S.371, D.387, W.392, S.393, R.394, L.396, E.400 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.371, B:S.371, B:S.393, B:S.393, B:R.394 Salt bridges: B:E.400 pi-Stacking: B:W.392, B:W.392, B:W.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mas-Droux, C. et al., A Novel Organization of Act Domains in Allosteric Enzymes Revealed by the Crystal Structure of Arabidopsis Aspartate Kinase. Plant Cell (2006)

Release Date

2006-05-30

Peptides

ASPARTOKINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ASPARTOKINASE