SMTL ID : 8w0j.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-trimer

Ligands

3 x YHT: 5'-O-{(S)-hydroxy[(prop-2-yn-1-yl)oxy]phosphoryl}adenosine(Non-covalent)

YHT.1: 16 residues within 4Å: Chain A: I.340, 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: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 YHT.14: 14 residues within 4Å: Chain B: I.340, 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: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 YHT.24: 14 residues within 4Å: Chain C: I.340, 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 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: S.80, Y.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.80 Water bridges: A:W.81, A:W.81 GOL.3: 6 residues within 4Å: Chain A: E.35, T.36, F.41, G.458, V.459, P.461 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.36, A:G.458 GOL.4: 4 residues within 4Å: Chain A: S.90, G.91 Chain B: A.117, F.118 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.91, B:F.118 GOL.5: 5 residues within 4Å: Chain A: H.137, E.147, Q.175, Y.249, W.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.137, A:E.147, A:Q.175 Water bridges: A:Y.249 GOL.15: 2 residues within 4Å: Chain B: S.80, Y.110 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.80, B:Y.110 Water bridges: B:W.81, B:W.81 GOL.16: 5 residues within 4Å: Chain B: E.35, T.36, G.458, V.459, P.461 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.35, B:T.36 GOL.25: 7 residues within 4Å: Chain C: E.35, T.36, F.41, G.458, V.459, V.460, P.461 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.35, C:E.35, C:T.36, C:T.36, C:V.460 GOL.26: 3 residues within 4Å: Chain B: H.86 Chain C: S.80, Y.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.110, C:Y.110

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain A: K.57, Y.60, E.61, Y.469, P.470 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.57, A:K.57 PGE.7: 6 residues within 4Å: Chain A: A.195, G.196, R.222, E.361, G.362, T.363 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.222 PGE.17: 6 residues within 4Å: Chain B: Y.56, K.57, Y.60, E.61, Y.469, P.470 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.57

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

SO4.8: 4 residues within 4Å: Chain A: D.550, I.644, R.646, R.650 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.550, A:R.646 Salt bridges: A:R.650 SO4.9: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.105 SO4.10: 3 residues within 4Å: Chain A: K.643, I.644, R.646 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.644, A:I.644 Salt bridges: A:R.646 SO4.11: 4 residues within 4Å: Chain A: R.395, S.421, D.423, I.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.421 Salt bridges: A:R.395 SO4.12: 3 residues within 4Å: Chain A: Q.68, K.89, D.500 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.68, A:Q.68 Salt bridges: A:K.89 SO4.13: 5 residues within 4Å: Chain A: E.77, L.78, R.115, L.352, L.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.352 Salt bridges: A:R.115 SO4.20: 4 residues within 4Å: Chain B: R.392, S.421, D.423, I.424 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.392, B:S.421, B:S.421 SO4.21: 4 residues within 4Å: Chain B: P.67, Q.68, K.89, D.500 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.68 Salt bridges: B:K.89 SO4.22: 6 residues within 4Å: Chain A: D.82, H.83 Chain B: D.82, H.83 Chain C: D.82, H.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.82 Salt bridges: B:H.83 SO4.23: 5 residues within 4Å: Chain B: S.201, R.205, T.294, S.295, P.301 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.205 SO4.27: 5 residues within 4Å: Chain C: F.197, S.201, R.205, S.295, P.301 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.205 SO4.28: 3 residues within 4Å: Chain C: R.395, S.421, D.423 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.421, C:S.421 Salt bridges: C:R.395 SO4.29: 3 residues within 4Å: Chain C: Q.68, K.89, D.500 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.68 Salt bridges: C:K.89

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

CL.18: 1 residues within 4Å: Chain B: R.618 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: T.300, K.515 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 a propyne 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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