SMTL ID : 3ei8.1

Crystal structure of K270N variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with LL-DAP: External aldimine form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 13 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, R.278 Chain B: Y.94, N.309 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.152, A:Y.152, A:N.209, A:Y.240 Hydrogen bonds: A:A.128, A:K.129, A:N.209, A:Y.240, A:S.267, A:S.267, A:S.269, B:N.309 Water bridges: A:S.269, A:N.270, B:Y.94 Salt bridges: A:R.278 pi-Stacking: A:Y.152

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

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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.81, S.92, N.313, Q.316, A.317 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.81, A:S.92 Water bridges: A:S.92, A:S.92, A:N.313, A:Q.316, A:Q.316 GOL.4: 11 residues within 4Å: Chain A: F.111, Y.112, S.238, A.241, M.242, R.250, S.251, E.264, A.266, Y.271, W.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.112, A:S.238, A:R.250 GOL.5: 6 residues within 4Å: Chain A: T.110, F.111, Y.112, G.113, L.115, E.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.254 GOL.8: 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, B:S.92 Water bridges: B:N.313 GOL.9: 11 residues within 4Å: Chain B: F.111, Y.112, S.238, A.241, M.242, R.250, S.251, E.264, A.266, Y.271, W.281 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.112, B:S.238, B:R.250, B:Y.271 Water bridges: B:S.238, B:Y.271 GOL.10: 7 residues within 4Å: Chain B: K.109, T.110, F.111, Y.112, G.113, L.115, E.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.113, B:E.254 Water bridges: B:T.110

1 x PL5: (2S,6S)-2-amino-6-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}heptanedioic acid(Non-covalent)

PL5.6: 21 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, R.278, R.404 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.39, B:F.39, B:I.63, B:Y.152, A:Y.94 Hydrogen bonds: B:G.64, B:A.128, B:K.129, B:N.209, B:Y.240, B:S.267, B:S.269, A:Y.94, A:E.97, A:N.309 Water bridges: B:S.269, B:N.270, 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

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