SMTL ID : 3eib.1

Crystal structure of K270N variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: G.127, A.128, K.129, Y.152, C.205, N.209, D.237, Y.240, S.267, S.269, N.270, R.278 Chain B: Y.94, N.309 Ligands: SO4.2 17 PLIP interactions: 2 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:Y.94, B:N.309, A:A.128, A:K.129, A:N.209, A:S.267, A:S.267, A:S.269, A:N.270 Hydrophobic interactions: A:Y.152, A:N.209, A:Y.240 Water bridges: A:Y.152, A:Y.240, A:S.269 Salt bridges: A:R.278 pi-Stacking: A:Y.152 PLP.5: 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, Y.240, S.267, S.269, N.270, R.278 Ligands: SO4.6 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.152, B:N.209 Hydrogen bonds: B:A.128, B:K.129, B:N.209, B:S.267, B:S.267, B:S.269, B:N.270, A:Y.94, A:N.309 Water bridges: B:A.239, B:Y.240, B:S.269 Salt bridges: B:R.278 pi-Stacking: B:Y.152

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

SO4.2: 8 residues within 4Å: Chain A: F.39, I.63, G.64, Y.152, N.209, Y.240, R.404 Ligands: PLP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.64, A:N.209 Water bridges: A:Y.240, A:Y.240, A:N.270 Salt bridges: A:R.404 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 SO4.6: 8 residues within 4Å: Chain B: F.39, I.63, G.64, Y.152, N.209, Y.240, R.404 Ligands: PLP.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.64, B:Y.152, B:N.209, B:N.209 Water bridges: B:Y.240, A:Y.94 Salt bridges: B:R.404 SO4.7: 4 residues within 4Å: Chain B: K.101, R.104, D.119, D.120 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.101, B:K.101 Salt bridges: B:K.101, B:R.104 SO4.8: 2 residues within 4Å: Chain B: G.176, N.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.177 Water bridges: B:I.178

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: K.81, S.92, A.100, N.313, Q.316, A.317 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.81, A:S.92 Water bridges: A:S.92, A:N.313, A:Q.316, A: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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