SMTL ID : 8g0u.1

Crystal Structure of Acetyl-CoA synthetase in complex with an isopropyl ester AMP inhibitor from Cryptococcus neoformans H99

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: W.91, Y.92, Y.120 Chain B: D.94, K.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.94 EDO.2: 4 residues within 4Å: Chain A: Y.138, T.183, Q.185, R.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.138, A:Q.185, A:R.260 EDO.4: 4 residues within 4Å: Chain B: W.91, Y.92, Y.120 Chain C: E.113 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.94 EDO.5: 5 residues within 4Å: Chain B: Y.138, T.183, Q.185, R.260, R.261 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.138, B:T.183, B:Q.185, B:R.260 EDO.7: 5 residues within 4Å: Chain A: K.96, E.113 Chain C: W.91, Y.92, Y.120 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain C: T.183, Q.185, R.260 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.183, C:Q.185, C:R.260 Water bridges: C:R.147, C:W.184

3 x YHQ: 5'-O-{(R)-hydroxy[(propan-2-yl)oxy]phosphoryl}adenosine(Non-covalent)

YHQ.3: 16 residues within 4Å: Chain A: W.348, I.349, T.350, V.425, G.426, E.427, P.428, D.450, T.451, Y.452, W.453, M.454, T.455, D.541, I.553, R.556 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.348, A:I.349, A:V.425, A:W.453 Hydrogen bonds: A:G.426, A:T.451, A:T.455, A:D.541, A:D.541, A:R.556 Water bridges: A:T.455, A:T.455, A:S.652, A:S.652 pi-Stacking: A:Y.452, A:Y.452 YHQ.6: 16 residues within 4Å: Chain B: W.348, I.349, T.350, V.425, G.426, E.427, P.428, D.450, T.451, Y.452, W.453, M.454, T.455, D.541, I.553, R.556 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.348, B:I.349, B:V.425, B:W.453 Hydrogen bonds: B:G.426, B:T.451, B:T.455, B:D.541, B:D.541, B:R.556 Water bridges: B:W.348, B:T.455, B:T.455, B:S.652 pi-Stacking: B:Y.452, B:Y.452 YHQ.9: 14 residues within 4Å: Chain C: I.349, T.350, V.425, G.426, E.427, P.428, D.450, T.451, Y.452, W.453, M.454, T.455, D.541, I.553 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.425, C:W.453 Hydrogen bonds: C:G.426, C:T.451, C:Y.452, C:Y.452, C:W.453, C:T.455, C:D.541 pi-Stacking: C:Y.452

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Crystal Structure of Acetyl-CoA synthetase in complex with an isopropyl ester AMP inhibitor from Cryptococcus neoformans H99. To be published

Release Date

2023-02-15

Peptides

Acetyl-coenzyme A synthetase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Acetyl-coenzyme A synthetase

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