SMTL ID : 5luc.4 (3 other biounits)

Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.8 Angstrom; internal aldimine with PLP in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: S.92, G.93, H.94, W.119, G.167, S.169, N.194, V.196, A.197, Q.219, K.220 Chain B: Y.271, H.273, T.274 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.119, A:V.196, A:K.220 Hydrogen bonds: A:G.93, A:H.94, A:S.169, A:N.194, A:Q.219, B:Y.271, B:T.274, B:T.274 Salt bridges: A:H.94 pi-Stacking: A:W.119 PLP.3: 14 residues within 4Å: Chain A: Y.271, H.273, T.274 Chain B: S.92, G.93, H.94, W.119, G.167, S.169, N.194, V.196, A.197, Q.219, K.220 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.119, B:V.196, B:A.197, B:K.220 Hydrogen bonds: B:G.93, B:H.94, B:S.169, B:N.194, B:Q.219, A:Y.271, A:T.274, A:T.274 Salt bridges: B:H.94 pi-Stacking: B:W.119

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.2: 6 residues within 4Å: Chain A: K.256, W.257, N.260, D.265, Q.267, M.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.260, A:D.265 Water bridges: A:F.261 BTB.4: 6 residues within 4Å: Chain B: K.256, W.257, N.260, D.265, Q.267, M.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.260, B:D.265 Water bridges: B:F.261

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

2017-09-20

Peptides

Serine--pyruvate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
T

Serine--pyruvate aminotransferase

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