SMTL ID : 8v4r.1

Crystal structure of Acetyl-CoA synthetase 2 in complex with AMP and CoA from Candida albicans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

3 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 16 residues within 4Å: Chain A: 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, G.556, R.558 Ligands: ACY.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.417, A:D.441, A:W.444, A:Q.445, A:T.446, A:T.446, 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 AMP.5: 15 residues within 4Å: Chain B: I.340, 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 B Hydrogen bonds: B:G.417, B:T.442, B:W.444, B:Q.445, B:T.446, B:T.446, B:T.446, B:D.532, B:R.547, B:R.558 Water bridges: B:T.341 Salt bridges: B:R.558 pi-Stacking: B:Y.443, B:Y.443 AMP.8: 15 residues within 4Å: Chain C: I.340, 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 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.417, C:D.441, C:Q.445, C:T.446, C:T.446, C:T.446, C:D.532, C:R.547, C:N.553, C:R.558 Salt bridges: C:R.558 pi-Stacking: C:Y.443, C:Y.443

3 x COA: COENZYME A(Non-covalent)

COA.2: 17 residues within 4Å: Chain A: F.194, A.195, G.196, R.222, R.225, T.227, A.334, G.335, D.336, T.341, P.364, S.555, H.557, R.618, P.623, F.624 Ligands: ACY.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.222, A:A.334, A:D.336, A:D.336, A:S.555, A:S.555 Salt bridges: A:R.222, A:R.225, A:R.618 pi-Cation interactions: A:R.222 COA.6: 9 residues within 4Å: Chain B: F.194, A.195, G.196, R.222, R.225, D.336, R.618, P.623, F.624 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.336 Salt bridges: B:R.222, B:R.225, B:R.618 COA.9: 7 residues within 4Å: Chain C: F.194, G.196, R.222, R.225, R.618, P.623, F.624 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.222, C:R.225 Salt bridges: C:R.222, C:R.225, C:R.618 pi-Cation interactions: C:R.222, C:R.222

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 7 residues within 4Å: Chain A: I.340, T.341, V.416, G.417, W.444 Ligands: AMP.1, COA.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.340, A:W.444 Hydrogen bonds: A:T.341, A:W.444

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.115, H.116, L.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.115 GOL.7: 3 residues within 4Å: Chain B: R.115, H.116, L.352 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jezewski, A.J. et al., A single Leishmania adenylate forming enzyme of the ANL superfamily generates both acetyl- and acetoacetyl-CoA. J.Biol.Chem. (2024)

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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