SMTL ID : 8w0h.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: K.76, F.85 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: F.85 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain C: K.76 Ligand excluded by PLIP

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

YHQ.2: 16 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, 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:R.558 Salt bridges: A:R.558 pi-Stacking: A:Y.443, A:Y.443 YHQ.8: 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, R.558 15 PLIP interactions: 15 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:T.446, B:D.532, B:D.532, B:R.547 Salt bridges: B:R.558 pi-Stacking: B:Y.443, B:Y.443 YHQ.13: 16 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, R.558 14 PLIP interactions: 14 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 Salt bridges: C:R.558 pi-Stacking: C:Y.443, C:Y.443

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: K.162, G.163, G.187, S.282, D.287, P.288 Chain B: Q.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.162, A:G.163 PG4.4: 5 residues within 4Å: Chain A: K.57, Y.60, E.61, K.65, Y.469 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.57, A:Y.60, A:K.65, A:K.65 PG4.9: 6 residues within 4Å: Chain B: K.162, G.163, G.187, D.287, P.288 Chain C: Q.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.162, B:P.288 PG4.10: 5 residues within 4Å: Chain B: K.57, Y.60, E.61, K.65, Y.469 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.57, B:Y.60, B:K.65, B:K.65 PG4.14: 7 residues within 4Å: Chain A: Q.156 Chain C: K.162, G.163, G.187, S.282, D.287, P.288 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.162, C:G.163, C:G.187, C:S.282 PG4.15: 6 residues within 4Å: Chain C: V.53, K.57, Y.60, E.61, K.65, Y.469 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.57, C:Y.60, C:K.65, C:K.65

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

PGE.5: 6 residues within 4Å: Chain A: S.90, G.91, T.92 Chain B: A.117, P.121, D.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.91 PGE.11: 7 residues within 4Å: Chain B: S.90, G.91, T.92, D.97 Chain C: P.121, G.142, R.146 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.142, C:R.146, B:G.91 PGE.16: 8 residues within 4Å: Chain A: A.117, P.121, G.142, R.146 Chain C: S.90, G.91, T.92, D.97 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.142, A:R.146, C:G.91, C:D.97

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

SO4.6: 3 residues within 4Å: Chain A: E.105 Chain B: E.105 Chain C: E.105 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.105

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 (trigonal form). 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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