SMTL ID : 5ofy.1

Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 14 residues within 4Å: Chain A: S.81, G.82, H.83, W.108, G.156, S.158, N.183, V.185, A.186, Q.208, K.209 Chain B: Y.260, T.263 Ligands: DIO.2 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.185, A:A.186, A:K.209 Hydrogen bonds: A:G.82, A:H.83, A:S.158, A:N.183, A:Q.208, B:T.263, B:T.263 Salt bridges: A:H.83 pi-Stacking: A:W.108 Water bridges: B:T.263 PLP.3: 14 residues within 4Å: Chain A: Y.260, T.263 Chain B: S.81, G.82, H.83, W.108, G.156, S.158, N.183, V.185, A.186, Q.208, K.209 Ligands: DIO.4 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.185, B:A.186, B:K.209 Hydrogen bonds: B:G.82, B:H.83, B:S.158, B:N.183, B:Q.208, B:K.209, A:Y.260, A:T.263, A:T.263, A:T.263 Salt bridges: B:H.83 pi-Stacking: B:W.108

2 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.2: 9 residues within 4Å: Chain A: P.28, G.29, K.209, M.348, L.351, R.360 Chain B: Y.260, T.263 Ligands: PLP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.360, A:R.360 DIO.4: 9 residues within 4Å: Chain A: Y.260, T.263 Chain B: P.28, G.29, K.209, M.348, L.351, R.360 Ligands: PLP.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.360, B:R.360

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giardina, G. et al., Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis. Sci Rep (2017)

Release Date

2017-09-27

Peptides

Serine--pyruvate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine--pyruvate aminotransferase