SMTL ID : 2z1z.1

Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana complexed with L-malate ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x MLT: D-MALATE(Non-covalent)

MLT.1: 10 residues within 4Å: Chain A: F.39, I.63, G.64, Y.152, N.209, K.270, R.404 Chain B: Y.94, N.309 Ligands: PLP.2 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.63 Hydrogen bonds: A:G.64, A:N.209, A:K.270, B:Y.94, B:N.309 Salt bridges: A:K.129, A:K.270, A:R.404

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)(Covalent)

PLP.2: 17 residues within 4Å: Chain A: G.127, A.128, K.129, Y.152, Y.155, C.205, N.209, D.237, A.239, Y.240, S.267, S.269, K.270, R.278 Chain B: Y.94, N.309 Ligands: MLT.1 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.152, A:N.209 Hydrogen bonds: A:A.128, A:K.129, A:N.209, A:Y.240, A:S.267, A:S.269, B:Y.94, B:Y.94, B:N.309 Salt bridges: A:R.278 pi-Stacking: A:Y.152 PLP.3: 15 residues within 4Å: Chain A: Y.94, N.309 Chain B: G.127, A.128, K.129, Y.152, C.205, N.209, D.237, A.239, Y.240, S.267, S.269, K.270, R.278 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.128, B:Y.152, B:N.209, B:A.239, B:K.270 Hydrogen bonds: B:A.128, B:K.129, B:N.209, B:Y.240, B:S.267, B:S.267, B:S.269, A:N.309 Water bridges: B:A.239, A:Y.94 Salt bridges: B:K.270, B:R.278 pi-Stacking: B:Y.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, N. et al., Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia. J.Mol.Biol. (2007)

Release Date

2007-07-17

Peptides

LL-diaminopimelate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LL-diaminopimelate aminotransferase

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