SMTL ID : 7knp.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-trimer

Ligands

3 x WT7: 5'-O-[(S)-butoxy(hydroxy)phosphoryl]adenosine(Non-covalent)

WT7.1: 16 residues within 4Å: Chain A: I.349, T.350, V.425, G.426, E.427, P.428, D.450, T.451, Y.452, W.453, M.454, T.455, E.456, D.541, I.553, R.556 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.349, A:V.425, A:W.453, A:W.453 Hydrogen bonds: A:G.426, A:D.450, A:T.455, A:T.455, A:R.556 pi-Stacking: A:Y.452, A:Y.452 WT7.7: 15 residues within 4Å: Chain B: 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.349, B:V.425, B:W.453, B:W.453 Hydrogen bonds: B:G.426, B:D.450, B:T.455, B:T.455, B:R.556 Water bridges: B:D.541 pi-Stacking: B:Y.452, B:Y.452 WT7.14: 13 residues within 4Å: Chain C: I.349, T.350, V.425, G.426, E.427, P.428, T.451, Y.452, W.453, M.454, T.455, D.541, I.553 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.349, C:V.425 Hydrogen bonds: C:G.426, C:T.451, C:W.453, C:T.455, C:T.455 pi-Stacking: C:Y.452, C:Y.452

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

EDO.2: 6 residues within 4Å: Chain A: D.90, W.91, Y.92, Y.120 Chain B: K.96, E.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.90, A:D.90 Water bridges: A:W.91 EDO.3: 6 residues within 4Å: Chain A: K.329, A.334, H.335, P.336, N.362, I.364 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: A.83, K.84, E.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.84, A:K.84 EDO.5: 3 residues within 4Å: Chain A: R.86, F.95, K.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.86, A:R.86, A:K.96 EDO.8: 4 residues within 4Å: Chain B: D.90, W.91, Y.120 Chain C: E.113 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.90 Water bridges: B:W.91 EDO.9: 5 residues within 4Å: Chain B: K.329, A.334, H.335, P.336, N.362 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.362 EDO.10: 5 residues within 4Å: Chain A: P.284 Chain B: V.314, T.517, Y.519, R.520 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.520 Water bridges: B:R.520, B:R.520 EDO.11: 3 residues within 4Å: Chain B: R.86, F.95, K.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.86, B:R.86, B:K.96 EDO.12: 6 residues within 4Å: Chain B: V.27, H.28, L.30, A.544, W.552, K.554 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.28 Water bridges: B:K.554, B:K.554 EDO.15: 6 residues within 4Å: Chain A: K.96, E.113 Chain C: D.90, W.91, Y.92, Y.120 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.90 Water bridges: C:W.91, A:D.94 EDO.16: 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.17: 3 residues within 4Å: Chain C: R.86, F.95, K.96 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.86, C:R.86, C:F.95 Water bridges: C:A.82

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

PO4.6: 3 residues within 4Å: Chain A: H.57, K.329, Y.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.330 Salt bridges: A:H.57, A:K.329 PO4.13: 3 residues within 4Å: Chain B: H.57, K.329, Y.330 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.57, B: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'-butylphosphate from Cryptococcus neoformans var. grubii serotype A (H99). To Be Published

Release Date

2020-12-23

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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