SMTL ID : 8w0c.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-trimer

Ligands

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

YHF.1: 16 residues within 4Å: Chain A: I.340, T.341, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.340, A:W.444, A:W.444 Hydrogen bonds: 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 Water bridges: A:E.418 Salt bridges: A:R.558 YHF.5: 14 residues within 4Å: Chain B: I.340, T.341, G.417, E.418, P.419, D.441, T.442, Y.443, W.444, Q.445, T.446, D.532, I.544, R.547 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.340, B:W.444 Hydrogen bonds: 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 YHF.11: 14 residues within 4Å: Chain C: I.340, T.341, G.417, E.418, P.419, D.441, T.442, Y.443, W.444, Q.445, T.446, D.532, I.544, R.547 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.340, C:W.444 Hydrogen bonds: C:T.442, C:W.444, C:Q.445, C:T.446, C:T.446, C:D.532, C:D.532, C:R.547 Water bridges: C:E.418 pi-Stacking: C:Y.443

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

NA.2: 3 residues within 4Å: Chain A: H.83 Chain C: H.83 Ligands: NA.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.82 NA.6: 1 residues within 4Å: Ligands: NA.2 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Water bridges: A:E.105, A:S.282, B:E.105, B:S.282, C:E.105, C:S.282

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

SO4.3: 3 residues within 4Å: Chain A: R.646, R.647, 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 SO4.9: 6 residues within 4Å: Chain B: G.299, T.300, K.515, R.647, R.650, K.651 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.300, B:T.300 Salt bridges: B:K.515, B:R.650, B:K.651 SO4.10: 6 residues within 4Å: Chain B: A.334, G.335, D.336, W.339, T.341, V.416 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.336 Water bridges: B:A.387 SO4.12: 4 residues within 4Å: Chain C: F.197, S.201, R.205, P.301 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.204 Salt bridges: C:R.205 SO4.13: 6 residues within 4Å: Chain A: A.117, P.121, G.142 Chain C: S.90, G.91, D.97 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.91, C:D.97 Water bridges: C:T.92, C:T.92, C:D.97

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 1 residues within 4Å: Chain B: R.618 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: H.83 Chain B: D.82, H.83, D.84 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:H.83, C:H.83 Hydrogen bonds: B:D.84

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 cyclopentyl ester AMP 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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