SMTL ID : 8bit.1

Crystal structure of acyl-CoA synthetase from Metallosphaera sedula in complex with Coenzyme A and acetyl-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 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: 18 residues within 4Å: Chain A: K.256, W.259, 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, D.459, R.461 Ligands: COA.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.256, A:W.259 Hydrogen bonds: A:G.328, A:D.349, A:G.352, A:Q.353, A:T.354, A:T.354, A:T.354, A:D.435, A:K.456 Salt bridges: A:K.456, A:K.456, A:R.461 pi-Stacking: A:Y.351 6R9.3: 16 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, D.459, R.461 Ligands: COA.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.328, B:D.349, B:G.352, B:Q.353, B:T.354, B:T.354, B:D.435 Salt bridges: B:K.456, B:K.456, B:R.461 pi-Stacking: B:Y.351

2 x COA: COENZYME A(Non-covalent)

COA.2: 19 residues within 4Å: Chain A: T.134, N.135, S.250, A.251, W.254, A.255, K.256, Y.277, G.279, K.280, L.281, P.301, Q.307, S.458, D.459, Y.460, R.490, P.524 Ligands: 6R9.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.301, A:D.459 Hydrogen bonds: A:T.134, A:N.135, A:A.251, A:L.281, A:Q.307, A:S.458, A:D.459, A:R.490 Salt bridges: A:R.490 COA.4: 20 residues within 4Å: Chain B: T.134, N.135, S.250, A.251, W.254, A.255, K.256, Y.277, K.280, L.281, P.301, T.303, A.304, Q.307, S.458, D.459, Y.460, R.490, P.524 Ligands: 6R9.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.301, B:T.303 Hydrogen bonds: B:T.134, B:N.135, B:A.251, B:Y.277, B:L.281, B:Q.307, B:S.458, B:D.459, B:R.490

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

4-hydroxybutyrate--CoA ligase 1

Related Entries With Identical Sequence