SMTL ID : 8aie.1

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense complexed with D-cycloserine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

1 x LCS: [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

LCS.1: 22 residues within 4Å: Chain A: T.36, H.50, R.53, R.138, K.144, Y.148, E.174, G.175, S.176, H.177, S.178, T.179, L.197, G.199, T.200, T.201, T.235, G.236, T.237, V.238, K.239 Ligands: PMP.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.148, A:T.200, A:T.200, A:T.201, A:T.201, A:T.237, A:T.237, A:V.238, A:K.239 Water bridges: A:T.36, A:T.36, A:R.53, A:T.179, A:R.202 Salt bridges: A:H.50, A:R.53

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.2: 16 residues within 4Å: Chain A: R.53, R.138, K.144, Y.148, E.174, H.177, S.178, T.179, L.197, G.199, T.200, T.201, T.235, G.236, T.237 Ligands: LCS.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.197 Hydrogen bonds: A:Y.148, A:T.200, A:T.200, A:T.201, A:T.201, A:T.237, A:T.237 Water bridges: A:R.53, A:T.179, A:R.202, A:T.237 Salt bridges: A:H.50, A:R.53 PMP.4: 16 residues within 4Å: Chain B: H.50, R.53, K.144, Y.148, E.174, G.175, S.176, H.177, S.178, T.179, L.197, T.200, T.201, G.236, T.237 Ligands: M7L.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.148, B:L.197 Hydrogen bonds: B:Y.148, B:S.176, B:T.200, B:T.201, B:T.237 Water bridges: B:R.53, B:R.53, B:R.202 Salt bridges: B:H.50, B:R.53

1 x M7L: 3-azanyloxy-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanoic acid(Non-covalent)

M7L.3: 24 residues within 4Å: Chain A: R.29 Chain B: F.34, T.36, H.50, R.53, R.138, K.144, Y.148, E.174, G.175, S.176, H.177, S.178, T.179, L.197, G.199, T.200, T.201, T.235, G.236, T.237, V.238, K.239 Ligands: PMP.4 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.36, B:K.144, B:K.144, B:Y.148, B:S.176, B:T.200, B:T.200, B:T.201, B:T.237, B:V.238, B:K.239, A:R.29, A:R.29 Water bridges: B:R.53, B:T.179, B:R.202 Salt bridges: B:H.50, B:R.53, B:K.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shilova, S.A. et al., 3D Structure of D-Аmino Acid Тransaminase from Aminobacterium colombiense in Complex with D-Cycloserine. Crystallography Reports (2023)

Release Date

2022-11-16

Peptides

Aminotransferase class IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminotransferase class IV

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