SMTL ID : 8biq.1

Crystal structure of acyl-COA synthetase from Metallosphaera sedula in complex with acetyl-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

3 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: G.328, E.329, P.330, D.349, F.350, Y.351, G.352, Q.353, T.354, D.435, F.447, R.450, K.456, R.461 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.328, A:F.350, A:G.352, A:Q.353, A:T.354, A:T.354, A:D.435, A:R.450, A:K.456 Salt bridges: A:K.456, A:R.461 pi-Stacking: A:Y.351 AMP.2: 14 residues within 4Å: Chain B: G.328, E.329, P.330, D.349, F.350, Y.351, G.352, Q.353, T.354, D.435, F.447, R.450, K.456, R.461 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.328, B:F.350, B:Q.353, B:T.354, B:T.354, B:T.354, B:D.435, B:R.450, B:K.456 Salt bridges: B:K.456, B:R.461 pi-Stacking: B:Y.351 AMP.4: 14 residues within 4Å: Chain D: G.328, E.329, P.330, D.349, F.350, Y.351, G.352, Q.353, T.354, D.435, F.447, R.450, K.456, R.461 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.328, D:D.349, D:Q.353, D:T.354, D:T.354, D:T.354, D:D.435, D:R.450 Salt bridges: D:K.456, D:R.461 pi-Stacking: D:Y.351, D:F.447

1 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)

6R9.3: 14 residues within 4Å: Chain C: G.328, E.329, P.330, D.349, F.350, Y.351, G.352, Q.353, T.354, D.435, F.447, R.450, K.456, R.461 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.328, C:D.349, C:G.352, C:Q.353, C:T.354, C:T.354, C:D.435, C:R.450 Salt bridges: C:K.456, C:K.456, C:R.461 pi-Stacking: C:Y.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Capra, N. et al., Adapting an acyl CoA ligase from Metallosphaera sedula for lactam formation by structure-guided protein engineering. Front Catal (2024)

Release Date

2023-11-15

Peptides

4-hydroxybutyrate--CoA ligase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

4-hydroxybutyrate--CoA ligase 1

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