SMTL ID : 8w0b.1

Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a cyclopropyl AMP ester inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x YHK: 5'-O-[(R)-(cyclopropyloxy)(hydroxy)phosphoryl]adenosine(Non-covalent)

YHK.1: 17 residues within 4Å: Chain A: I.340, T.341, V.416, G.417, E.418, P.419, D.441, T.442, Y.443, W.444, Q.445, T.446, D.532, I.544, R.547, N.553, R.558 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.340, A:V.416 Hydrogen bonds: A:G.417, A:T.442, A:W.444, A:Q.445, A:T.446, A:T.446, A:D.532, A:D.532, A:R.547, A:N.553 Salt bridges: A:R.558 pi-Stacking: A:Y.443, A:Y.443 YHK.6: 16 residues within 4Å: Chain B: I.340, T.341, V.416, G.417, E.418, P.419, D.441, T.442, Y.443, W.444, Q.445, T.446, D.532, I.544, R.547 Ligands: SO4.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.340, B:V.416, B:W.444 Hydrogen bonds: B:G.417, B:T.442, B:W.444, B:Q.445, B:T.446, B:D.532, B:D.532, B:R.547 pi-Stacking: B:Y.443, B:Y.443 YHK.14: 15 residues within 4Å: Chain C: I.340, T.341, V.416, G.417, E.418, P.419, D.441, T.442, Y.443, W.444, Q.445, T.446, D.532, I.544, R.547 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.340, C:V.416, C:W.444 Hydrogen bonds: C:G.417, C:T.442, C:W.444, C:Q.445, C:T.446, C:T.446, C:D.532, C:D.532, C:R.547 pi-Stacking: C:Y.443, C:Y.443

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: H.83 Chain B: H.83 Chain C: H.83 Ligands: NA.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:D.82, B:E.105, C:E.105 NA.7: 1 residues within 4Å: Ligands: NA.2 8 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B, 1 interactions with chain A Water bridges: C:E.105, C:E.105, C:S.282, B:E.105, B:E.105, B:E.105, B:S.282, A:S.282

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

SO4.3: 3 residues within 4Å: Chain A: D.550, R.646, R.650 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.646, A:R.647 Salt bridges: A:R.650 SO4.4: 3 residues within 4Å: Chain A: H.49, E.77, K.320 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.320 SO4.5: 5 residues within 4Å: Chain A: S.80, W.81, D.82, Y.110 Chain C: H.86 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Salt bridges: C:H.86 Hydrogen bonds: A:W.81 Water bridges: A:S.80, A:D.82, A:N.111 SO4.9: 2 residues within 4Å: Chain B: V.614, R.618 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.618 SO4.10: 5 residues within 4Å: Chain B: T.300, K.515, R.647, R.650, K.651 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.300, B:T.300, B:R.647 Salt bridges: B:K.515, B:R.650, B:K.651 SO4.11: 6 residues within 4Å: Chain B: S.90, G.91, D.97 Chain C: A.117, F.118, P.121 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.91 Water bridges: C:R.146 SO4.12: 3 residues within 4Å: Chain B: W.339 Ligands: YHK.6, SO4.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.339 SO4.13: 4 residues within 4Å: Chain B: W.339, T.341, V.416 Ligands: SO4.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.341, B:T.341 SO4.15: 6 residues within 4Å: Chain C: F.197, S.201, D.204, R.205, S.295, P.301 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.204 Salt bridges: C:R.205

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: H.83 Chain B: H.83 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.84 Water bridges: C:H.83, C:H.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a cyclopropyl AMP ester inhibitor. To be published

Release Date

2024-02-21

Peptides

Acetyl-coenzyme A synthetase 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Acetyl-coenzyme A synthetase 2

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