SMTL ID : 8rpl.2 (1 other biounit)

AMP-forming acetyl-CoA synthetase from Chloroflexota bacterium with bound acetyl AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-trimer

Ligands

3 x 6R9: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate(Non-covalent)

6R9.1: 19 residues within 4Å: Chain A: V.337, T.338, V.413, G.414, E.415, P.416, D.438, T.439, W.440, W.441, Q.442, T.443, A.463, D.525, I.537, G.539, R.540, K.546, R.551 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.441 Hydrogen bonds: A:G.414, A:T.439, A:W.440, A:W.441, A:Q.442, A:T.443, A:T.443, A:R.540, A:K.546 Salt bridges: A:K.546, A:K.546, A:R.551 6R9.4: 20 residues within 4Å: Chain B: T.291, V.337, T.338, V.413, G.414, E.415, P.416, D.438, T.439, W.440, W.441, Q.442, T.443, A.463, D.525, I.537, G.539, R.540, K.546, R.551 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.413, B:W.441 Hydrogen bonds: B:G.414, B:T.439, B:W.441, B:Q.442, B:T.443, B:T.443, B:R.540, B:K.546 Salt bridges: B:K.546, B:K.546, B:R.551 6R9.7: 18 residues within 4Å: Chain C: V.337, T.338, V.413, G.414, E.415, P.416, D.438, T.439, W.440, W.441, Q.442, T.443, A.463, D.525, I.537, R.540, K.546, R.551 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.441 Hydrogen bonds: C:G.414, C:T.439, C:W.441, C:Q.442, C:T.443, C:T.443, C:R.540, C:K.546 Salt bridges: C:K.546, C:K.546, C:R.551

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 10 residues within 4Å: Chain A: P.596, T.597, E.598, A.601, K.605, D.619, E.620, L.621, E.622, F.623 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.621 Salt bridges: A:E.598, A:K.605 EPE.5: 10 residues within 4Å: Chain B: P.596, T.597, E.598, A.601, K.605, D.619, E.620, L.621, E.622, F.623 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.596, B:L.621 Salt bridges: B:E.598, B:E.598, B:K.605 EPE.8: 9 residues within 4Å: Chain C: P.596, T.597, E.598, A.601, K.605, D.619, E.620, L.621, F.623 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.621 Salt bridges: C:E.598, C:K.605

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: V.562, S.563, H.564, P.565, V.567, R.591 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.562, A:H.564, A:V.567, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain B: V.562, H.564, P.565, V.567, R.591 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:V.562, B:H.564, B:V.567, H2O.3, H2O.4

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 5 residues within 4Å: Chain C: V.562, H.564, P.565, V.567, R.591 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.567, C:R.591

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, C. et al., Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule. Nat Commun (2024)

Release Date

2024-06-19

Peptides

Acetate--CoA ligase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

Acetate--CoA ligase

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