SMTL ID : 3eia.1

Crystal structure of K270Q variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with L-Glu: External aldimine form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.101, R.104, D.119, D.120 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.119 Salt bridges: A:R.104 SO4.4: 4 residues within 4Å: Chain B: K.101, R.104, D.119, D.120 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.101, B:R.104

2 x PL6: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid(Non-covalent)

PL6.2: 21 residues within 4Å: Chain A: Y.37, F.39, I.63, G.64, G.127, A.128, K.129, Y.152, Y.155, C.205, N.209, D.237, Y.240, S.267, S.269, Q.270, R.278, Y.364, R.404 Chain B: Y.94, N.309 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.39, A:I.63, A:I.63, A:Y.152, A:N.209, A:Y.240, B:Y.94 Hydrogen bonds: A:Y.37, A:G.64, A:A.128, A:K.129, A:Y.152, A:N.209, A:S.267, A:S.269, A:Y.364, B:Y.94, B:N.309 Water bridges: A:S.269, A:L.279 Salt bridges: A:K.129, A:R.278, A:R.404 pi-Stacking: A:Y.152 PL6.3: 22 residues within 4Å: Chain A: Y.94, N.309 Chain B: Y.37, F.39, I.63, G.64, G.127, A.128, K.129, Y.152, Y.155, C.205, N.209, D.237, A.239, Y.240, S.267, S.269, Q.270, R.278, Y.364, R.404 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.39, B:I.63, B:I.63, B:Y.152, B:N.209, B:Y.240, A:Y.94 Hydrogen bonds: B:Y.37, B:G.64, B:A.128, B:K.129, B:Y.152, B:N.209, B:S.267, B:S.269, B:Y.364, A:N.309 Water bridges: B:S.269, B:L.279 Salt bridges: B:K.129, B:R.278, B:R.404 pi-Stacking: B:Y.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, N. et al., Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana. J.Mol.Biol. (2008)

Release Date

2008-10-14

Peptides

LL-diaminopimelate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LL-diaminopimelate aminotransferase