SMTL ID : 5eqc.1

Structure of the ornithine aminotransferase from Toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of PLP at the protein active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 6 residues within 4Å: Chain A: R.63, Y.73, E.419, E.420, D.423, R.427 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.63, A:R.63, A:Y.73, A:E.419 Water bridges: A:T.417, A:R.427, A:R.427 Salt bridges: A:R.427

4 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.2: 4 residues within 4Å: Chain A: V.234, R.369, G.370, R.371 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.370, A:R.371 Water bridges: A:R.351 BGC.8: 2 residues within 4Å: Chain B: E.35, D.36 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.35, B:E.35, B:D.36, B:D.36 Water bridges: B:T.33, B:E.35 BGC.9: 4 residues within 4Å: Chain B: A.93, C.96, R.97, E.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.97 Salt bridges: B:R.97 BGC.10: 4 residues within 4Å: Chain B: H.88, P.89, E.337, V.415 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.337 Water bridges: B:E.337 Salt bridges: B:H.88

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 6 residues within 4Å: Chain A: M.124, F.125, L.269, L.270, D.273, H.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.124, A:D.273 Water bridges: A:L.269

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 10 residues within 4Å: Chain A: N.134, T.135, G.136, A.137, G.285, K.286, I.295 Chain B: T.316, F.317 Ligands: PLP.7 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.316, B:T.316, A:G.136, A:K.286, A:I.295, A:I.295 Water bridges: B:G.314, B:S.315, B:F.317 PEG.5: 9 residues within 4Å: Chain A: Y.188, N.189, N.190, F.191, G.192, F.194 Chain B: Y.152, P.159, D.160 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.190, A:F.191, A:G.192, A:G.192 Water bridges: B:D.160 PEG.6: 4 residues within 4Å: Chain A: D.112 Chain B: R.26, L.31, I.67 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.26 Water bridges: B:S.57 PEG.12: 10 residues within 4Å: Chain A: T.316, F.317 Chain B: N.134, T.135, G.136, A.137, G.285, K.286, I.295 Ligands: PLP.13 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.136, B:A.137, B:K.286, B:I.295, B:I.295, A:T.316 Water bridges: A:E.138, A:T.316, A:T.316

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

PLP.7: 12 residues within 4Å: Chain A: T.135, G.136, A.137, Y.171, W.172, E.224, D.257, I.259, Q.260, K.286 Chain B: T.316 Ligands: PEG.4 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.316, B:T.316, B:T.316, A:G.136, A:A.137, A:Q.260, A:K.286 Water bridges: B:F.317, A:Y.171, A:R.174, A:E.224 Hydrophobic interactions: A:I.259 PLP.13: 13 residues within 4Å: Chain A: S.315, T.316 Chain B: T.135, G.136, A.137, Y.171, W.172, E.224, D.257, I.259, Q.260, K.286 Ligands: PEG.12 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.171, B:Q.260 Hydrogen bonds: B:T.135, B:T.135, B:G.136, B:A.137, B:Q.260, B:K.286, A:T.316, A:T.316, A:T.316 Water bridges: B:Y.171, A:F.317

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

BTB.11: 6 residues within 4Å: Chain B: M.124, F.125, G.126, L.269, D.273, H.278 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.278 Water bridges: B:H.278, B:H.278 Salt bridges: B:D.273

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.14: 2 residues within 4Å: Chain B: C.353, R.356 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippova, E.V. et al., Structure of the ornithine aminotransferase from Toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of PLP at the protein active site. To Be Published

Release Date

2016-02-24

Peptides

Ornithine aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ornithine aminotransferase, mitochondrial

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