SMTL ID : 8v4p.1

Crystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-allylphosphate from Candida albicans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.639, R.640, S.641 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.640, A:S.641 SO4.2: 3 residues within 4Å: Chain A: K.643, I.644, R.646 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.644 Salt bridges: A:R.646 SO4.3: 4 residues within 4Å: Chain A: Q.68, H.86, T.87, V.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.86, A:V.88 Water bridges: A:Q.68, A:K.89 SO4.4: 5 residues within 4Å: Chain A: R.392, 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 SO4.5: 1 residues within 4Å: Ligands: SO4.6 No protein-ligand interaction detected (PLIP) SO4.6: 5 residues within 4Å: Chain A: E.105 Chain B: E.105 Chain C: E.105 Ligands: SO4.5, SO4.15 10 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, 4 interactions with chain A Water bridges: C:E.105, C:S.282, C:S.282, B:S.282, B:S.282, A:S.282, A:S.282, A:S.282, A:S.282 Hydrogen bonds: B:E.105 SO4.12: 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:T.300 Salt bridges: B:K.515, B:R.650, B:K.651 SO4.13: 6 residues within 4Å: Chain B: T.341, A.387, V.416, G.417 Ligands: SO4.14, WPO.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.341, B:T.341 SO4.14: 3 residues within 4Å: Chain B: W.339 Ligands: SO4.13, WPO.18 No protein-ligand interaction detected (PLIP) SO4.15: 8 residues within 4Å: Chain A: D.82, H.83 Chain B: D.82, H.83 Chain C: D.82, H.83 Ligands: SO4.6, SO4.16 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Water bridges: B:E.105, C:E.105 Salt bridges: B:H.83, A:H.83 SO4.16: 3 residues within 4Å: Chain B: H.83 Chain C: H.83 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain C Water bridges: C:H.83, C:D.84

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

CL.7: 1 residues within 4Å: Chain A: K.76 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: R.647, K.651 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: R.205, P.301 Ligand excluded by PLIP

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

WPO.9: 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:R.547, A:N.553, A:R.558 Salt bridges: A:R.558 pi-Stacking: A:Y.443, A:Y.443 WPO.10: 13 residues within 4Å: Chain A: P.171, M.172, F.194, A.195, G.196, R.222, T.227, D.336, E.361, G.362, T.363, P.364, P.623 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:M.172, A:R.222, A:D.336 Water bridges: A:L.170, A:G.338, A:E.361 Salt bridges: A:R.222 pi-Cation interactions: A:R.222 WPO.18: 18 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: SO4.13, SO4.14, PG4.19 13 PLIP interactions: 13 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:R.547 Water bridges: B:D.532, B:D.532 pi-Stacking: B:Y.443, B:Y.443 WPO.20: 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 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.340, C:W.444 Hydrogen bonds: C:G.417, C:D.441, C:Q.445, C:T.446, C:T.446, C:D.532, C:R.547 pi-Stacking: C:Y.443, C:Y.443 WPO.21: 12 residues within 4Å: Chain C: P.171, M.172, F.194, A.195, G.196, R.222, T.227, D.336, E.361, G.362, T.363, P.364 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.172, C:T.227

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

PG4.11: 7 residues within 4Å: Chain A: S.90, G.91, T.92, D.97 Chain B: A.117, F.118, P.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.91 Water bridges: A:N.95 PG4.19: 9 residues within 4Å: Chain B: Q.445, E.447, T.519, Y.520, F.529, T.530, G.531, R.547 Ligands: WPO.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.547, B:R.547 Water bridges: B:T.519

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lovell, S. et al., Crystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-allylphosphate from Candida albicans. To be published

Release Date

2023-12-06

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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