SMTL ID : 5vwr.1

E.coli Aspartate aminotransferase-(1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP)-alpha-ketoglutarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x PL6: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid(Non-covalent)

PL6.1: 19 residues within 4Å: Chain A: I.13, L.14, I.33, G.34, G.102, G.103, T.104, W.130, N.183, D.211, Y.214, S.243, S.245, K.246, R.254, F.348, R.374 Chain B: Y.65, R.280 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.14, A:I.33, B:Y.65 Hydrogen bonds: A:G.34, A:G.103, A:T.104, A:T.104, A:N.183, A:Y.214, A:S.243, A:S.245, A:K.246, B:S.284 Salt bridges: A:K.246, A:R.254, A:R.374, B:R.280 pi-Stacking: A:W.130, A:W.130 Water bridges: B:Y.65, B:S.284 PL6.7: 19 residues within 4Å: Chain A: Y.65, R.280 Chain B: I.13, L.14, I.33, G.34, G.102, G.103, T.104, W.130, N.183, D.211, Y.214, S.243, S.245, K.246, R.254, F.348, R.374 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.14, B:I.33, A:Y.65 Hydrogen bonds: B:G.34, B:G.103, B:T.104, B:N.183, B:S.243, B:S.245, B:K.246, A:Y.65, A:S.284 Salt bridges: B:K.246, B:R.254, B:R.374, A:R.280 pi-Stacking: B:W.130, B:W.130 Water bridges: A:Y.65, A:S.284

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: K.134, N.138, E.143, V.144, R.145 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.134, A:N.138, A:V.144, A:V.144, A:R.145 Water bridges: A:N.138, A:L.142 GOL.3: 2 residues within 4Å: Chain A: P.72, R.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.76, A:R.76 Water bridges: A:E.73 GOL.4: 2 residues within 4Å: Chain A: R.315, Q.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.315, A:R.315 GOL.5: 6 residues within 4Å: Chain A: G.67, I.68, K.276 Chain B: L.14, A.17, D.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.68 Water bridges: A:K.276 GOL.6: 8 residues within 4Å: Chain A: I.68, S.273, K.276, A.277 Chain B: A.8, P.9, A.10, D.11 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.276, A:K.276, B:P.9, B:D.11, B:D.11 GOL.8: 5 residues within 4Å: Chain B: K.134, N.138, E.143, V.144, R.145 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.134, B:N.138, B:V.144, B:V.144, B:R.145 Water bridges: B:N.138, B:L.142 GOL.9: 2 residues within 4Å: Chain B: P.72, R.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.76, B:R.76 Water bridges: B:E.73 GOL.10: 2 residues within 4Å: Chain B: R.315, Q.316 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.315, B:R.315 GOL.11: 6 residues within 4Å: Chain A: L.14, A.17, D.18 Chain B: G.67, I.68, K.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.68 Water bridges: B:K.276 GOL.12: 8 residues within 4Å: Chain A: A.8, P.9, A.10, D.11 Chain B: I.68, S.273, K.276, A.277 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.9, A:D.11, A:D.11, A:D.11, B:K.276, B:K.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mascarenhas, R. et al., Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover. Biochemistry (2017)

Release Date

2017-09-13

Peptides

Aspartate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aspartate aminotransferase

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