SMTL ID : 8ayk.1

Crystal structure of D-amino acid aminotrensferase from Aminobacterium colombiense complexed with D-glutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x PW0: (~{Z})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pent-2-enedioic acid(Non-covalent)

PW0.1: 24 residues within 4Å: Chain A: 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 Chain B: R.29 Ligands: PMP.2 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.36, A:L.197, A:T.237 Hydrogen bonds: A:K.144, A:Y.148, A:Y.148, A:H.177, A:T.200, A:T.200, A:T.201, A:T.201, A:T.237, A:V.238, A:K.239 Water bridges: A:R.53, A:R.53, A:T.179, A:R.202, A:K.239, B:R.29 Salt bridges: A:H.50, A:R.53, A:K.144, A:K.239, B:R.29 PW0.3: 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 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.36, B:L.197 Hydrogen bonds: B:T.36, B:T.36, B:K.144, B:Y.148, B:T.200, B:T.200, B:T.201, B:T.237, B:V.238, B:K.239 Water bridges: B:R.53, B:R.53, B:T.179, B:R.202 Salt bridges: B:H.50, B:R.53, B:K.144, B:H.177, B:K.239, A:R.29

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

PMP.2: 19 residues within 4Å: Chain A: 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 Ligands: PW0.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.197 Hydrogen bonds: A:K.144, A:Y.148, A:S.176, A:H.177, A:T.200, A:T.200, A:T.201, A:T.201, A:T.237 Water bridges: A:R.53, A:R.53, A:T.179, B:R.29 Salt bridges: A:H.50, A:R.53 PMP.4: 19 residues within 4Å: Chain B: 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 Ligands: PW0.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.197 Hydrogen bonds: B:K.144, B:Y.148, B:E.174, B:H.177, B:T.200, B:T.201, B:T.237 Water bridges: B:T.36, B:R.53, B:R.53, B:T.179, B:R.202 Salt bridges: B:H.50, B:R.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shilova, S.A. et al., To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense. Molecules (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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