SMTL ID : 9ctd.1

CtfAB F42TS45C mutant co-crystallized with acetyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

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

ACT.1: 9 residues within 4Å: Chain A: F.24, L.25, N.50, S.74, H.75, Q.98 Chain C: E.46, G.126 Ligands: ACT.10 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.24, A:L.25, A:H.75 Hydrogen bonds: A:N.50, A:Q.98 Salt bridges: A:H.75 Water bridges: C:A.68 ACT.4: 11 residues within 4Å: Chain B: F.24, L.25, N.50, D.51, S.74, H.75, Q.98 Chain D: E.46, A.68, G.126 Ligands: ACT.14 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.24, B:L.25, B:H.75 Hydrogen bonds: B:N.50, B:Q.98, D:A.68 Salt bridges: B:H.75 ACT.10: 9 residues within 4Å: Chain A: H.75, Q.98 Chain C: E.46, M.125, G.126, G.127, A.128, L.131 Ligands: ACT.1 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.127, A:Q.98 ACT.14: 9 residues within 4Å: Chain B: H.75, Q.98 Chain D: E.46, M.125, G.126, G.127, A.128, L.131 Ligands: ACT.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.98, D:G.127

11 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: T.18, H.146, A.147, D.148, K.181 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.147 PEG.3: 4 residues within 4Å: Chain A: I.38, R.39, N.41, N.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.38, A:N.41 PEG.5: 5 residues within 4Å: Chain B: T.18, H.146, A.147, D.148, K.181 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.146, B:H.146, B:A.147 PEG.6: 7 residues within 4Å: Chain B: V.3, V.187, I.190, I.211, V.212, T.213 Ligands: PEG.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.213 Water bridges: B:T.213, B:T.213 PEG.7: 5 residues within 4Å: Chain B: E.188, E.189, I.190, T.213 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain B Water bridges: B:I.190 PEG.8: 6 residues within 4Å: Chain B: F.54, R.57 Chain D: G.69, A.70, S.71, Y.72 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.57, B:R.57, D:Y.72 PEG.9: 6 residues within 4Å: Chain A: F.54, R.57 Chain C: G.69, A.70, S.71, Y.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.57, A:R.57 PEG.11: 8 residues within 4Å: Chain C: R.92, G.93, G.94, T.133, G.134, A.135, K.136, R.164 No protein-ligand interaction detected (PLIP) PEG.12: 4 residues within 4Å: Chain C: P.56, K.57, Y.60, T.74 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.57 Water bridges: C:A.55 PEG.15: 5 residues within 4Å: Chain D: A.55, P.56, K.57, Y.60, T.74 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.57 Water bridges: D:P.54, D:A.55 PEG.16: 8 residues within 4Å: Chain D: R.92, G.93, G.94, T.133, G.134, A.135, K.136, R.164 No protein-ligand interaction detected (PLIP)

2 x COA: COENZYME A(Non-covalent)

COA.13: 18 residues within 4Å: Chain C: K.4, I.25, G.26, L.27, P.28, G.102, G.103, L.104, Q.105, N.114, I.117, K.120, M.121, T.143, A.146, K.147, K.151, L.158 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.104 Hydrogen bonds: C:L.27, C:L.104, C:K.151 Water bridges: C:G.103, C:Q.105, C:T.143 Salt bridges: C:K.4, C:K.4, C:K.147, C:K.151 COA.17: 16 residues within 4Å: Chain D: K.4, G.26, L.27, P.28, G.102, G.103, L.104, Q.105, N.114, I.117, M.121, T.143, A.146, K.147, K.151, L.158 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.104, D:N.114 Hydrogen bonds: D:L.27, D:L.104, D:K.151 Water bridges: D:G.103, D:Q.105, D:T.143 Salt bridges: D:K.4, D:K.4, D:K.147, D:K.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bing, R.G. et al., Structural and Kinetic Characterization of an Acetoacetyl-Coenzyme A: Acetate Coenzyme A Transferase from the Extreme Thermophile Thermosipho melanesiensis. Biochem.J. (2025)

Release Date

2025-02-05

Peptides

3-oxoacid CoA-transferase, A subunit: AB
3-oxoacid CoA-transferase, B subunit: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
C

D
B

3-oxoacid CoA-transferase, A subunit

3-oxoacid CoA-transferase, B subunit

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