SMTL ID : 8w0l.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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, R.558 Ligands: COA.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.416, A:W.444 Hydrogen bonds: A:G.417, A:D.441, A:W.444, A:Q.445, A:T.446, A:D.532, A:D.532, A:R.547 Salt bridges: A:R.558 pi-Stacking: A:Y.443, A:Y.443 YHT.15: 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.25: 17 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, N.553, R.558 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:D.532, C:D.532, C:R.547 Salt bridges: C:R.558 pi-Stacking: C:Y.443, C:Y.443

2 x COA: COENZYME A(Non-covalent)

COA.2: 19 residues within 4Å: Chain A: F.194, A.195, G.196, R.222, D.336, W.339, T.341, P.364, A.387, T.389, A.390, L.393, S.555, G.556, H.557, R.618, P.623, F.624 Ligands: YHT.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.387, A:L.393 Hydrogen bonds: A:R.222, A:D.336, A:S.555, A:G.556, A:H.557 Salt bridges: A:R.222, A:R.618 pi-Cation interactions: A:R.222 COA.26: 7 residues within 4Å: Chain C: F.194, G.196, R.222, D.336, R.618, P.623, F.624 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.222, C:D.336, C:P.623 Salt bridges: C:R.222, C:R.618 pi-Cation interactions: C:R.222

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.35, T.36, F.41, G.458, V.459, V.460, P.461 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.36, A:T.36, A:V.460 GOL.4: 6 residues within 4Å: Chain A: S.90, G.91 Chain B: A.117, F.118, P.121, L.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.90, A:G.91 GOL.5: 7 residues within 4Å: Chain A: H.137, L.139, E.147, Q.175, I.178, Y.249, W.267 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.147, A:Q.175, A:W.267 GOL.16: 6 residues within 4Å: Chain B: E.35, T.36, F.41, G.458, V.459, P.461 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.35, B:T.36

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

PGE.6: 4 residues within 4Å: Chain A: K.57, Y.60, E.61, Y.469 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.57, A:K.57 PGE.17: 6 residues within 4Å: Chain B: Y.56, K.57, Y.60, E.61, Y.469, P.470 No protein-ligand interaction detected (PLIP)

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

SO4.7: 3 residues within 4Å: Chain A: D.550, R.646, R.650 Ligand excluded by PLIP SO4.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: K.643, I.644, R.646 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: R.395, S.421, D.423, I.424 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: Q.68, H.86, T.87, V.88 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: E.77, L.78, R.115, H.116, L.352, L.353 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: R.647, K.651 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: L.79, S.80 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: R.395, S.421, D.423, I.424 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain B: S.80 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: P.67, Q.68, K.89, D.500 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain A: H.83 Chain B: D.82, H.83 Chain C: D.82, H.83 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain B: S.201, R.205, T.294, S.295, P.301 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain C: R.395, S.421, D.423, I.424 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: P.67, Q.68, K.89, D.500 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain C: S.80 Ligand excluded by PLIP

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

CL.18: 1 residues within 4Å: Chain B: R.618 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: T.300, K.515, K.651 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 and CoA. 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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