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

Citryl-CoA lyase core module of Chlorobium limicola ATP citrate lyase in complex with acetyl-CoA and L-malate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: Q.256, E.257 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.257, H2O.3

2 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.2: 12 residues within 4Å: Chain A: R.242 Chain C: H.69, V.73, F.104, H.145, R.146, V.147, R.156, V.196, F.218, R.222 Ligands: ACO.3 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.69, C:R.222, C:R.222 Salt bridges: C:H.69, C:H.69, C:H.145, C:H.145, C:R.156, C:R.222, A:R.242 LMR.5: 11 residues within 4Å: Chain B: R.242 Chain D: H.69, V.73, F.104, H.145, R.146, V.147, R.156, F.218, R.222 Ligands: ACO.6 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:H.69, D:R.222, D:R.222 Water bridges: D:H.145 Salt bridges: D:H.69, D:H.69, D:H.145, D:H.145, D:R.156, D:R.222, B:R.242

2 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 24 residues within 4Å: Chain A: R.239, L.240 Chain C: P.102, R.103, F.104, G.105, A.107, P.139, V.140, P.141, G.142, I.143, G.144, H.145, R.146, R.156, K.189, N.191, L.192, N.195, V.196, D.197, F.218 Ligands: LMR.2 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:A.107, C:V.196, C:F.218 Hydrogen bonds: C:R.103, C:G.105, C:V.140, C:V.140, C:G.142, C:I.143, C:I.143, C:N.191, C:N.195 Water bridges: C:H.145, C:K.189, A:L.240 Salt bridges: C:R.146, C:K.189, A:R.239, A:R.239 pi-Stacking: C:P.139 ACO.6: 25 residues within 4Å: Chain B: R.239, L.240 Chain D: P.102, R.103, F.104, G.105, A.107, P.139, V.140, P.141, G.142, I.143, G.144, H.145, R.146, R.156, K.189, N.191, L.192, N.195, V.196, D.197, F.218, R.222 Ligands: LMR.5 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.218 Hydrogen bonds: D:R.103, D:G.105, D:V.140, D:V.140, D:G.142, D:I.143, D:I.143, D:N.191, D:N.195, B:R.239 Water bridges: D:H.145 Salt bridges: D:R.146, D:K.189

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 7 residues within 4Å: Chain B: Y.244 Chain C: E.6, P.7, L.8, I.9, R.10 Chain D: N.249 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.6 Water bridges: C:R.10, C:R.10, D:N.249

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 4 residues within 4Å: Chain D: M.117, D.121, Y.122, W.132 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.121 Water bridges: D:W.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verschueren, K.H.G. et al., Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle. Nature (2019)

Release Date

2019-04-10

Peptides

ATP-citrate lyase alpha-subunit: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

ATP-citrate lyase alpha-subunit

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