SMTL ID : 3ei5.1

Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with PLP-Glu: an external aldimine mimic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

PGU.1: 22 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, A.239, Y.240, S.267, S.269, K.270, R.278, Y.364, R.404 Chain B: Y.94, N.309 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.39, 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:N.209, A:Y.240, A:S.267, A:S.269, B:Y.94, B:Y.94, B:N.309 Water bridges: A:S.269, A:S.269 Salt bridges: A:K.129, A:K.270, A:R.278, A:R.404 pi-Stacking: A:Y.152 PGU.5: 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, K.270, R.278, Y.364, R.404 24 PLIP interactions: 21 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.39, 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:Y.240, B:S.267, B:S.269, B:Y.364, A:Y.94, A:N.309 Water bridges: B:S.269 Salt bridges: B:K.129, B:K.270, B:R.278, B:R.404 pi-Stacking: B:Y.152

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.81, S.92, A.100, N.313, A.317, L.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.81, A:S.92, A:S.92 Water bridges: A:N.313 GOL.4: 6 residues within 4Å: Chain A: F.111, M.242, L.328, M.331, H.332, I.335 No protein-ligand interaction detected (PLIP) GOL.6: 7 residues within 4Å: Chain B: K.81, S.92, A.100, N.313, Q.316, A.317, L.320 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.81, B:S.92 Water bridges: B:S.92, B:N.313 GOL.8: 6 residues within 4Å: Chain B: M.242, Y.271, L.328, M.331, H.332, I.335 No protein-ligand interaction detected (PLIP)

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

SO4.3: 4 residues within 4Å: Chain A: K.101, R.104, D.119, D.120 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.101, A:R.104 SO4.7: 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

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

Related Entries With Identical Sequence