SMTL ID : 8w0d.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: H.83 Chain B: D.82, H.83 Ligands: NA.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.84, B:D.84

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

YHQ.2: 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.340, A:V.416, A:W.444 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 YHQ.8: 15 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 12 PLIP interactions: 12 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:T.446, B:D.532, B:D.532, B:R.547 pi-Stacking: B:Y.443, B:Y.443 YHQ.11: 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.3: 1 residues within 4Å: Chain A: E.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.105 Water bridges: A:S.282 NA.12: 3 residues within 4Å: Chain B: H.83 Chain C: H.83 Ligands: GOL.1 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: D.550, R.646, R.650 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.550, A:R.646, A:R.646 Salt bridges: A:R.650 SO4.5: 2 residues within 4Å: Chain A: R.647, K.651 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.647, A:K.651 SO4.9: 5 residues within 4Å: Chain B: 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, B:R.647 Salt bridges: B:K.515, B:R.650

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

CL.6: 1 residues within 4Å: Chain C: S.90 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: G.91 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: R.618 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: S.90 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: S.201, R.205 Ligand excluded by PLIP

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 an isopropyl 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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