SMTL ID : 5e3k.1

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 5JV: 4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid(Non-covalent)

5JV.1: 16 residues within 4Å: Chain A: Y.49, V.79, T.135, G.136, A.137, Y.171, W.172, E.224, E.229, D.257, I.259, Q.260, K.286 Chain B: G.314, S.315, T.316 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.79, A:Y.171, A:Y.171 Hydrogen bonds: A:Y.49, A:T.135, A:G.136, A:A.137, A:Y.171, A:Q.260, A:K.286, B:S.315, B:T.316, B:T.316, B:T.316 Water bridges: A:Y.171, B:G.314, B:F.317 5JV.8: 17 residues within 4Å: Chain A: G.314, S.315, T.316 Chain B: Y.49, V.79, T.135, G.136, A.137, Y.171, W.172, G.173, E.224, E.229, D.257, I.259, Q.260, K.286 17 PLIP interactions: 5 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:S.315, A:T.316, A:T.316, A:T.316, B:T.135, B:G.136, B:A.137, B:Y.171, B:Q.260, B:K.286 Water bridges: A:F.317, B:T.135, B:T.135, B:R.174 Hydrophobic interactions: B:V.79, B:Y.171, B:Q.260

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.404, R.406 Ligands: CO3.6 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.404, A:R.406 SO4.3: 6 residues within 4Å: Chain A: D.204, D.205, V.206, G.207, K.236, R.242 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.205, A:V.206, A:G.207 Water bridges: A:D.204, A:K.236, A:K.236, A:K.236 Salt bridges: A:K.236, A:R.242 SO4.4: 3 residues within 4Å: Chain A: A.348, R.351, R.355 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.351, A:D.352, A:R.355 Salt bridges: A:R.351, A:R.355 SO4.9: 6 residues within 4Å: Chain B: D.204, D.205, V.206, G.207, K.236, R.242 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.206, B:G.207 Water bridges: B:D.205, B:D.205, B:K.236 Salt bridges: B:K.236, B:R.242 SO4.10: 2 residues within 4Å: Chain B: R.404, R.406 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.404, B:R.406 SO4.11: 2 residues within 4Å: Chain B: R.18, K.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.19 Salt bridges: B:R.18 SO4.12: 1 residues within 4Å: Chain B: K.214 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.214 Salt bridges: B:K.214

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

PEG.5: 2 residues within 4Å: Chain A: R.119 Chain B: L.29 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.119, A:R.119, B:L.29 PEG.7: 6 residues within 4Å: Chain A: C.179, S.180, S.181, S.182, Y.188, F.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.180, A:S.182 PEG.15: 4 residues within 4Å: Chain B: S.180, S.182, F.194, L.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.180

3 x CO3: CARBONATE ION(Non-functional Binders)

CO3.6: 4 residues within 4Å: Chain A: T.183, T.184, F.185 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.183, A:F.185 CO3.13: 2 residues within 4Å: Chain B: P.196, G.197 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.197 Water bridges: B:F.198, B:F.198, B:F.198, B:F.198 CO3.14: 2 residues within 4Å: Chain B: R.351, R.355 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.351, B:R.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippova, E.V. et al., Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid. To Be Published

Release Date

2016-10-26

Peptides

Aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminotransferase

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