SMTL ID : 6pk1.1 (2 other biounits)

Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana in presence of serine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 17 residues within 4Å: Chain A: T.68, G.69, T.70, W.73, F.95, V.144, N.146, E.147, T.148, D.175, V.177, S.178, Q.200, K.201 Chain C: Y.249, T.250 Ligands: 3PY.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.95, A:V.177, A:V.177 Hydrogen bonds: A:T.68, A:G.69, A:T.70, A:T.70, A:W.73, A:T.148, A:Q.200, A:K.201, C:T.250 Water bridges: C:T.250 PLP.3: 16 residues within 4Å: Chain B: T.68, G.69, T.70, W.73, F.95, V.144, N.146, E.147, T.148, D.175, V.177, S.178, Q.200, K.201 Chain D: Y.249, T.250 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:F.95, B:V.144, B:V.177, B:V.177 Hydrogen bonds: B:T.68, B:T.68, B:G.69, B:T.70, B:T.70, B:W.73, B:T.148, B:Q.200, B:K.201, D:T.250, D:T.250 Water bridges: D:Y.35 PLP.4: 17 residues within 4Å: Chain A: Y.249, T.250 Chain C: T.68, G.69, T.70, W.73, F.95, V.144, N.146, E.147, T.148, D.175, V.177, S.178, Q.200, K.201 Ligands: 3PY.5 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.95, C:V.177, C:V.177 Hydrogen bonds: C:T.68, C:G.69, C:T.70, C:T.70, C:W.73, C:T.148, C:Q.200, C:K.201, A:T.250 Water bridges: A:T.250 PLP.6: 16 residues within 4Å: Chain B: Y.249, T.250 Chain D: T.68, G.69, T.70, W.73, F.95, V.144, N.146, E.147, T.148, D.175, V.177, S.178, Q.200, K.201 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:F.95, D:V.144, D:V.177, D:V.177 Hydrogen bonds: D:T.68, D:T.68, D:G.69, D:T.70, D:T.70, D:W.73, D:T.148, D:Q.200, D:K.201, B:T.250, B:T.250 Water bridges: B:Y.35

2 x 3PY: 3-HYDROXYPYRUVIC ACID(Non-covalent)

3PY.2: 11 residues within 4Å: Chain A: P.15, G.16, F.95, T.148, K.201, L.338, R.347 Chain C: Y.35, R.36, T.250 Ligands: PLP.1 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:P.15, A:K.201, C:R.36, C:T.250 Salt bridges: A:K.201, A:R.347, C:R.36 Water bridges: C:R.36, C:R.36 3PY.5: 11 residues within 4Å: Chain A: Y.35, R.36, T.250 Chain C: P.15, G.16, F.95, T.148, K.201, L.338, R.347 Ligands: PLP.4 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:R.36, A:T.250, C:P.15, C:K.201 Water bridges: A:R.36, A:R.36 Salt bridges: A:R.36, C:K.201, C:R.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liepman, A.H. et al., Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) FromArabidopsis thaliana. Front Plant Sci (2019)

Release Date

2019-10-23

Peptides

Serine--glyoxylate aminotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Serine--glyoxylate aminotransferase

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