SMTL ID : 7kqz.1

Crystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Coccidioides immitis RS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-trimer

Ligands

3 x WTA: 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine(Non-covalent)

WTA.1: 16 residues within 4Å: Chain A: I.342, T.343, V.417, G.418, E.419, P.420, D.442, T.443, Y.444, W.445, Q.446, T.447, D.533, I.545, R.548, R.559 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.342, A:V.417, A:W.445 Hydrogen bonds: A:G.418, A:T.443, A:W.445, A:Q.446, A:T.447, A:T.447, A:D.533, A:R.548 Water bridges: A:I.342, A:I.421 Salt bridges: A:R.559 pi-Stacking: A:Y.444, A:Y.444 WTA.7: 16 residues within 4Å: Chain B: I.342, T.343, V.417, G.418, E.419, P.420, D.442, T.443, Y.444, W.445, Q.446, T.447, D.533, I.545, R.548, R.559 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.342, B:V.417, B:W.445 Hydrogen bonds: B:G.418, B:T.443, B:W.445, B:Q.446, B:T.447, B:T.447, B:D.533, B:R.548 Water bridges: B:I.342, B:I.421 Salt bridges: B:R.559 pi-Stacking: B:Y.444, B:Y.444 WTA.13: 16 residues within 4Å: Chain C: I.342, T.343, V.417, G.418, E.419, P.420, D.442, T.443, Y.444, W.445, Q.446, T.447, D.533, I.545, R.548, R.559 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:I.342, C:V.417, C:W.445 Hydrogen bonds: C:G.418, C:T.443, C:W.445, C:Q.446, C:T.447, C:T.447, C:D.533, C:R.548 Water bridges: C:I.342, C:I.421 Salt bridges: C:R.559 pi-Stacking: C:Y.444, C:Y.444

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: L.62, R.76, M.77, D.80, Y.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.76 Water bridges: A:E.58, A:Y.323 EDO.3: 6 residues within 4Å: Chain A: K.86, D.89, G.106 Chain C: T.83, E.85, F.113 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.86, A:D.89 Water bridges: C:E.85, C:E.85 EDO.4: 7 residues within 4Å: Chain A: Y.131, R.140, I.176, P.177, E.178, F.252, R.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.140, A:R.140, A:E.178 EDO.5: 5 residues within 4Å: Chain A: R.140, I.142, E.146, E.150, F.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.140 Water bridges: A:E.178, A:E.178 EDO.6: 6 residues within 4Å: Chain A: D.80, L.81, R.118, H.119, L.354, L.355 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain B: L.62, R.76, M.77, D.80, Y.323 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.76 Water bridges: B:E.58, B:Y.323 EDO.9: 6 residues within 4Å: Chain A: T.83, E.85, F.113 Chain B: K.86, D.89, G.106 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.86, B:D.89 Water bridges: A:E.85, A:E.85 EDO.10: 7 residues within 4Å: Chain B: Y.131, R.140, I.176, P.177, E.178, F.252, R.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.140, B:R.140, B:E.178 EDO.11: 5 residues within 4Å: Chain B: R.140, I.142, E.146, E.150, F.181 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.140 Water bridges: B:E.178, B:E.178 EDO.12: 6 residues within 4Å: Chain B: D.80, L.81, R.118, H.119, L.354, L.355 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain C: L.62, R.76, M.77, D.80, Y.323 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.76 Water bridges: C:E.58, C:Y.323 EDO.15: 6 residues within 4Å: Chain B: T.83, E.85, F.113 Chain C: K.86, D.89, G.106 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.86, C:D.89 Water bridges: B:E.85, B:E.85 EDO.16: 7 residues within 4Å: Chain C: Y.131, R.140, I.176, P.177, E.178, F.252, R.254 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.140, C:R.140, C:E.178 EDO.17: 5 residues within 4Å: Chain C: R.140, I.142, E.146, E.150, F.181 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.140 Water bridges: C:E.178, C:E.178 EDO.18: 6 residues within 4Å: Chain C: D.80, L.81, R.118, H.119, L.354, L.355 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fox III, D. et al., Crystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Coccidioides immitis RS. to be published

Release Date

2020-12-16

Peptides

Acetyl-coenzyme A synthetase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Acetyl-coenzyme A synthetase

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