SMTL ID : 7tur.1

Joint X-ray/neutron structure of aspastate aminotransferase (AAT) in complex with pyridoxamine 5'-phosphate (PMP)

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

1 x PLA: 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID(Covalent)

PLA.1: 24 residues within 4Å: Chain A: V.19, F.20, V.39, G.40, G.109, G.110, T.111, L.114, W.142, H.145, H.191, N.196, D.224, A.226, Y.227, S.257, S.259, K.260, R.268, F.362, R.388 Chain B: Y.72, R.294, S.298 28 PLIP interactions: 4 interactions with chain B, 24 interactions with chain A Hydrogen bonds: B:Y.72, A:G.40, A:G.110, A:T.111, A:T.111, A:T.111, A:W.142, A:W.142, A:N.196, A:N.196, A:N.196, A:D.224, A:Y.227, A:S.257, A:S.259, A:S.259, A:K.260 Water bridges: B:S.298, B:S.298, A:S.225 Salt bridges: B:R.294, A:K.260, A:R.268, A:R.388 Hydrophobic interactions: A:G.40, A:W.142, A:W.142, A:K.260

1 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Covalent)

PMP.2: 18 residues within 4Å: Chain A: Y.72, S.298 Chain B: G.109, G.110, T.111, L.114, W.142, H.145, H.191, N.196, D.224, A.226, Y.227, S.257, S.259, K.260, R.268, F.362 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.142, B:W.142, B:N.196 Hydrogen bonds: B:G.110, B:T.111, B:T.111, B:T.111, B:N.196, B:N.196, B:D.224, B:Y.227, B:S.257, B:S.257, B:S.259, B:K.260, B:K.260, A:Y.72 Salt bridges: B:R.268 Water bridges: A:S.298, A:N.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drago, V.N. et al., An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction. Chem Sci (2022)

Release Date

2022-09-28

Peptides

Aspartate aminotransferase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate aminotransferase, cytoplasmic

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