SMTL ID : 7kno.1

Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x WTA: 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine(Non-covalent)

WTA.1: 15 residues within 4Å: Chain A: W.348, I.349, 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.349, A:V.425, A:W.453 Hydrogen bonds: A:G.426, A:T.451, A:T.455, A:T.455, A:D.541, A:R.556 Water bridges: A:T.455, A:T.455, A:D.541, A:S.652 pi-Stacking: A:Y.452, A:Y.452 WTA.7: 15 residues within 4Å: Chain B: W.348, I.349, 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:I.349, B:V.425, B:W.453 Hydrogen bonds: B:G.426, B:D.450, B:T.455, B:T.455, B:D.541, B:R.556 Water bridges: B:T.455, B:T.455, B:D.541, B:G.555, B:S.652 pi-Stacking: B:Y.452, B:Y.452 WTA.13: 16 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, R.556, R.567 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.425, C:W.453 Hydrogen bonds: C:G.426, C:T.451, C:W.453, C:T.455, C:T.455, C:D.541, C:R.556 Salt bridges: C:R.567 pi-Stacking: C:Y.452, C:Y.452

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

EDO.2: 6 residues within 4Å: Chain A: K.329, A.334, H.335, P.336, N.362, I.364 5 PLIP interactions: 5 interactions with chain A Water bridges: A:A.325, A:K.329, A:P.336, A:N.362, A:N.362 EDO.5: 6 residues within 4Å: Chain A: K.96, E.113 Chain C: D.90, W.91, Y.92, Y.120 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.96, C:D.90 Water bridges: A:D.94, C:W.91 EDO.6: 5 residues within 4Å: Chain A: D.90, W.91, Y.92, Y.120 Chain B: E.113 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.90, A:D.90 Water bridges: A:W.91, B:D.94 EDO.8: 5 residues within 4Å: Chain B: D.90, W.91, Y.120 Chain C: K.96, E.113 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.91, B:W.91 EDO.9: 6 residues within 4Å: Chain B: K.329, A.334, H.335, P.336, N.362, I.364 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.335 Water bridges: B:A.325, B:N.362 EDO.10: 3 residues within 4Å: Chain B: Y.62, D.548, Y.550 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.550, B:Y.550 EDO.14: 6 residues within 4Å: Chain C: K.329, A.334, H.335, P.336, N.362, I.364 4 PLIP interactions: 4 interactions with chain C Water bridges: C:A.325, C:P.336, C:N.362, C:N.362 EDO.15: 1 residues within 4Å: Chain C: R.232 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.232, C:R.232

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: T.307, K.311, R.524, T.528 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.307, A:T.307, A:T.307, A:T.528 Water bridges: A:T.528 Salt bridges: A:K.311, A:R.524 PO4.4: 3 residues within 4Å: Chain A: H.57, K.329, Y.330 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.330, A:Y.330 Water bridges: A:K.329, A:K.329 Salt bridges: A:H.57, A:K.329 PO4.11: 3 residues within 4Å: Chain B: K.311, R.524, T.528 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.311, B:R.524 PO4.12: 3 residues within 4Å: Chain B: H.57, K.329, Y.330 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.84 Salt bridges: B:H.57, B:K.329 PO4.16: 3 residues within 4Å: Chain C: H.57, K.329, Y.330 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.330 Salt bridges: C:H.57, C:K.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Cryptococcus neoformans var. grubii serotype A (H99). to be published

Release Date

2020-12-30

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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