SMTL ID : 5e5h.1

Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate and degradation products from the acetyl-CoA analogue dethiaacetyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: N.112, R.120, N.125 Chain B: G.443 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: V.196, R.354 Chain B: R.354 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: G.443 Chain B: N.112, R.120, N.125 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: R.354 Chain B: V.196, R.354 Ligand excluded by PLIP

2 x 0T1: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(propylamino)propyl]amino]butyl] hydrogen phosphate(Non-covalent)

0T1.3: 19 residues within 4Å: Chain A: F.92, Q.267, E.294, N.361, G.362, M.363, I.364, S.374, V.377, M.383, N.384, G.385, I.386, G.388, S.389, P.404, A.407, I.412 Ligands: ACE.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.92 Hydrogen bonds: A:G.362, A:I.364, A:N.384, A:G.388, A:S.389 Water bridges: A:V.273, A:S.374, A:G.385, A:S.389, A:K.408 0T1.10: 20 residues within 4Å: Chain B: F.92, V.270, G.271, N.272, V.273, N.361, G.362, M.363, I.364, S.374, V.377, M.383, N.384, G.385, I.386, S.389, P.404, A.407, K.408, I.412 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.92 Hydrogen bonds: B:N.272, B:N.272, B:G.362, B:I.364, B:N.384, B:K.408 Water bridges: B:V.270, B:V.270, B:S.374, B:G.385, B:G.385, B:G.388, B:S.389 Salt bridges: B:K.408

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.4: 7 residues within 4Å: Chain A: T.36, F.92, L.114, E.294, G.387, G.388 Ligands: 0T1.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.36, A:F.92, A:L.114 Hydrogen bonds: A:G.388

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 4 residues within 4Å: Chain A: R.200, D.202, R.310, I.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.200, A:D.202

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 7 residues within 4Å: Chain A: M.418, A.419, A.420, V.422 Chain B: M.418, A.419, V.422 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.419 Water bridges: B:A.419, A:A.419, A:V.422 IMD.7: 6 residues within 4Å: Chain A: T.487, L.490, S.491, Q.494 Chain B: L.486, T.487 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.490 Water bridges: A:L.490, A:L.490 IMD.12: 6 residues within 4Å: Chain A: V.190 Chain B: N.257, R.258, L.259, P.260, Y.397 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.397, B:Y.397 IMD.13: 6 residues within 4Å: Chain A: L.486, T.487 Chain B: T.487, L.490, S.491, Q.494 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:L.486, B:T.487, B:L.490

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 4 residues within 4Å: Chain B: T.36, S.71, T.94, R.228 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.71 Salt bridges: B:R.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murphy, J.R. et al., Functional Dissection of the Bipartite Active Site of the Class I Coenzyme A (CoA)-Transferase Succinyl-CoA:Acetate CoA-Transferase. Front Chem (2016)

Release Date

2016-05-18

Peptides

Succinyl-CoA:acetate CoA-transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Succinyl-CoA:acetate CoA-transferase

Related Entries With Identical Sequence