SMTL ID : 6hxk.1

Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 10 residues within 4Å: Chain A: H.69, V.73, F.104, G.105, R.155, D.195, F.230, R.234 Chain B: E.16 Chain C: R.254 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain A Salt bridges: C:R.254, A:H.69, A:H.69, A:R.234 Hydrogen bonds: A:G.105, A:D.195 Water bridges: A:G.106, A:A.107, A:R.155, A:R.234 FLC.4: 10 residues within 4Å: Chain A: E.16 Chain B: H.69, V.73, F.104, G.105, R.155, D.195, F.230, R.234 Chain D: R.254 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.105 Water bridges: B:A.107, B:R.155, B:R.234 Salt bridges: B:H.69, B:H.69, B:R.234, D:R.254 FLC.7: 10 residues within 4Å: Chain A: R.254 Chain C: H.69, V.73, F.104, G.105, R.155, D.195, F.230, R.234 Chain D: E.16 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain C Salt bridges: A:R.254, C:H.69, C:H.69, C:R.234 Hydrogen bonds: C:G.105 Water bridges: C:H.69, C:A.107, C:R.234 FLC.9: 10 residues within 4Å: Chain B: R.254 Chain D: H.69, V.73, R.103, F.104, G.105, R.155, D.195, F.230, R.234 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.73 Hydrogen bonds: D:G.105 Water bridges: D:H.69, D:A.107, D:R.155, D:R.155 Salt bridges: D:H.69, D:H.69, D:R.234, B:R.254

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: V.129, M.132, K.133, G.136, K.137, L.138, I.139 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.3: 7 residues within 4Å: Chain A: L.138, I.139, I.142, G.143, T.183, L.190 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.139, A:I.142 Water bridges: A:I.142 EDO.11: 9 residues within 4Å: Chain A: P.265, E.266 Chain D: A.24, G.25, M.26, L.44, Q.48, K.49, R.50 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.24 Water bridges: D:R.50

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

PGE.5: 10 residues within 4Å: Chain A: F.32, E.35, M.36, G.37, I.38 Chain B: Q.57, E.60, M.61, M.64, Y.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.35 Water bridges: A:I.38 PGE.10: 10 residues within 4Å: Chain C: F.32, E.35, M.36, G.37, I.38 Chain D: Q.57, E.60, M.61, M.64, Y.162 3 PLIP interactions: 3 interactions with chain C Water bridges: C:E.35, C:G.37, C:I.38

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 11 residues within 4Å: Chain C: Q.57, E.60, M.61, M.64, I.158, Y.162 Chain D: F.32, K.33, E.35, G.37, I.38 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.57 Water bridges: D:G.37

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

PEG.8: 2 residues within 4Å: Chain C: Q.165, H.166 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.165

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 synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ATP-citrate synthase

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