SMTL ID : 6zzk.1 (1 other biounit)

Crystal structure of the catalytic domain of C. glutamicum AceF (E2p) in ternary complex with CoA and dihydrolipoamide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 22 residues within 4Å: Chain A: R.46, K.50, N.60, T.62, Y.63, L.64, A.103, V.104, D.105, A.134, R.138, T.155, N.156, I.157, G.158, S.159, T.179, G.180, A.181, I.182 Chain C: G.216, A.217 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.64, A:A.134 Hydrogen bonds: A:N.60, A:T.62, A:Y.63, A:D.105, A:R.138, A:R.138, A:T.155, A:N.156, A:S.159, A:S.159, A:G.180, A:I.182 Water bridges: A:T.62, A:T.62, A:T.179, C:A.217 Salt bridges: A:R.46, A:K.50 COA.3: 22 residues within 4Å: Chain A: G.216, A.217 Chain B: R.46, K.50, N.60, T.62, Y.63, L.64, A.103, V.104, D.105, A.134, R.138, T.155, N.156, I.157, G.158, S.159, T.179, G.180, A.181, I.182 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.64, B:A.134 Hydrogen bonds: B:N.60, B:T.62, B:T.62, B:Y.63, B:D.105, B:R.138, B:R.138, B:T.155, B:T.155, B:N.156, B:S.159, B:S.159, B:G.180, B:I.182 Water bridges: B:T.62, B:L.64, B:T.179, A:A.217 Salt bridges: B:R.46, B:K.50 COA.5: 22 residues within 4Å: Chain B: G.216, A.217 Chain C: R.46, K.50, N.60, T.62, Y.63, L.64, A.103, V.104, D.105, A.134, R.138, T.155, N.156, I.157, G.158, S.159, T.179, G.180, A.181, I.182 20 PLIP interactions: 1 interactions with chain B, 19 interactions with chain C Water bridges: B:A.217, C:T.62, C:L.64 Hydrophobic interactions: C:L.64, C:A.134 Hydrogen bonds: C:N.60, C:T.62, C:T.62, C:Y.63, C:D.105, C:R.138, C:R.138, C:T.155, C:N.156, C:S.159, C:S.159, C:G.180, C:I.182 Salt bridges: C:R.46, C:K.50

3 x LPM: 6,8-DIMERCAPTO-OCTANOIC ACID AMIDE(Non-covalent)

LPM.2: 11 residues within 4Å: Chain A: T.17, T.21, L.110, L.111, T.112, P.167, I.168, V.170, I.176 Chain C: L.31, H.211 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.21, A:T.112, A:V.170, A:I.176 Hydrogen bonds: A:L.110 Water bridges: A:T.112 LPM.4: 11 residues within 4Å: Chain A: L.31, H.211 Chain B: T.17, T.21, L.110, L.111, T.112, P.167, I.168, V.170, I.176 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.21, B:T.112, B:V.170, B:I.176 Hydrogen bonds: B:L.110 Water bridges: B:T.112 LPM.6: 11 residues within 4Å: Chain B: L.31, H.211 Chain C: T.17, T.21, L.110, L.111, T.112, P.167, I.168, V.170, I.176 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.21, C:T.112, C:V.170, C:I.176 Hydrogen bonds: C:L.110 Water bridges: C:T.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruch, E.M. et al., Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-08-18

Peptides

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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