SMTL ID : 8ayj.1

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiens complexed with 3-aminooxypropionic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x OCF: 3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid(Non-covalent)(Covalent)

OCF.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 Chain B: R.29 Ligands: OCF.3, PLP.4 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.177, A:L.197 Hydrogen bonds: A:Y.148, A:S.178, A:T.200, A:T.201, A:T.201, A:T.237 Water bridges: A:R.53, A:R.53, A:T.179, A:R.202 Salt bridges: A:H.50, A:R.53, A:K.144, A:H.177, B:R.29 OCF.3: 15 residues within 4Å: Chain A: F.34, T.36, M.88, R.90, E.115, K.144, Y.148, Y.162, H.177, T.237, V.238, K.239 Chain B: R.29 Ligands: OCF.1, PLP.4 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.238, A:V.238 Hydrogen bonds: A:K.239, B:R.29 Water bridges: A:R.90, A:R.90 Salt bridges: A:R.90, A:K.144, A:H.177, B:R.29, B:R.29 OCF.5: 23 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 Ligands: PLP.6, OCF.7 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.177, B:L.197 Hydrogen bonds: B:T.36, B:Y.148, B:S.178, B:T.200, B:T.201, B:T.237 Water bridges: B:T.36, B:R.53, B:E.174, B:T.201, B:R.202 Salt bridges: B:H.50, B:R.53, B:K.144, A:R.29 OCF.7: 16 residues within 4Å: Chain A: R.29 Chain B: F.34, T.36, M.88, R.90, E.115, R.118, K.144, Y.148, Y.162, H.177, T.237, V.238, K.239 Ligands: OCF.5, PLP.6 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.238, B:V.238 Hydrogen bonds: B:T.36, B:T.36, B:T.36, B:Y.148, B:K.239, A:R.29 Water bridges: B:R.90, B:R.90 Salt bridges: B:R.90, B:R.118, B:K.144, B:H.177, A:R.29, A:R.29

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: M.46, Q.203, E.207, W.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.203 Water bridges: A:E.207

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.4: 19 residues within 4Å: Chain A: H.50, R.53, R.138, 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: OCF.1, OCF.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.197 Hydrogen bonds: A:S.176, A:S.178, A:T.200, A:T.201, A:T.201, A:T.237 Water bridges: A:R.53, A:R.53, A:T.179, A:R.202 Salt bridges: A:H.50, A:R.53 PLP.6: 19 residues within 4Å: Chain B: H.50, R.53, R.138, 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: OCF.5, OCF.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.197 Hydrogen bonds: B:Y.148, B:S.178, B:T.200, B:T.201, B:T.237 Water bridges: B:R.53, B:R.53, B:E.174, 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., In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity. Biochem.J. (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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