SMTL ID : 3ei6.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.101, R.104, D.119, D.120 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.120, A:D.120 Salt bridges: A:R.104 SO4.6: 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 SO4.8: 8 residues within 4Å: Chain B: F.111, Y.112, S.238, A.241, E.264, A.266, Y.271, W.281 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.238, B:Y.271

2 x PL4: (2S,6S)-2-amino-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]heptanedioic acid(Non-covalent)

PL4.2: 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, Y.240, S.267, S.269, K.270, R.278, Y.364, R.404 Chain B: Y.94, E.97, N.309 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.39, A:F.39, A:I.63, 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:K.270, A:Y.364, B:Y.94, B:E.97, B:N.309 Water bridges: A:K.129, A:K.129, A:S.267, A:S.269 Salt bridges: A:K.129, A:K.270, A:R.278, A:R.404 pi-Stacking: A:Y.152 PL4.5: 23 residues within 4Å: Chain A: Y.94, E.97, 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 27 PLIP interactions: 5 interactions with chain A, 22 interactions with chain B Hydrophobic interactions: A:Y.94, B:F.39, B:F.39, B:I.63, B:Y.152, B:N.209, B:Y.240 Hydrogen bonds: A:E.97, A:E.97, A:E.97, A:N.309, 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 Water bridges: B:S.269, B:L.279 Salt bridges: B:K.129, B:K.270, B:R.278, B:R.404 pi-Stacking: B:Y.152

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: K.81, S.92, A.100, N.313, Q.316, A.317, L.320 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.81, A:K.81, A:S.92, A:S.92 Water bridges: A:N.313 GOL.4: 4 residues within 4Å: Chain A: P.185, G.188, F.189, Y.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.185 GOL.7: 5 residues within 4Å: Chain B: K.81, A.100, N.313, Q.316, A.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.81, B:K.81 Water bridges: B:Q.316

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

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