SMTL ID : 6hxl.2 (1 other biounit)

Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate and CoASH (space group P21)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 20 residues within 4Å: Chain A: D.102, R.103, F.104, G.105, A.107, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.187, N.189, L.190, N.193, D.195 Chain C: L.252 Ligands: FLC.2 16 PLIP interactions: 1 interactions with chain C, 15 interactions with chain A Hydrophobic interactions: C:L.252 Hydrogen bonds: A:R.103, A:I.139, A:I.139, A:G.141, A:I.142, A:I.142, A:I.142, A:N.189, A:N.193 Water bridges: A:H.144, A:H.144, A:R.145, A:R.145 Salt bridges: A:R.145, A:K.187 COA.5: 21 residues within 4Å: Chain A: L.252 Chain C: D.102, R.103, F.104, G.105, A.107, K.133, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.187, N.189, L.190, N.193, D.195 Ligands: FLC.6 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.107, A:L.252 Hydrogen bonds: C:R.103, C:I.139, C:I.139, C:G.141, C:I.142, C:I.142, C:N.189, C:N.193 Water bridges: C:H.144, C:R.145, C:R.145, C:R.145, C:R.145, C:R.145 Salt bridges: C:K.133, C:R.145, C:K.187 COA.7: 16 residues within 4Å: Chain D: R.103, A.107, A.110, K.133, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.187, N.189, L.190, N.193 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:I.139, D:I.139, D:G.141, D:I.142, D:N.189 Water bridges: D:K.133, D:N.193 Salt bridges: D:K.133, D:K.187, D:K.187

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 15 residues within 4Å: Chain A: H.69, V.73, F.104, G.105, H.144, R.145, V.146, R.155, N.193, V.194, D.195, F.230, R.234 Chain C: R.254 Ligands: COA.1 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.73, A:F.230 Hydrogen bonds: A:H.69, A:G.105, A:H.144, A:R.155, A:R.155 Water bridges: A:H.144, A:R.234 Salt bridges: A:H.69, A:H.69, A:H.144, A:R.155, A:R.234, C:R.254 FLC.6: 15 residues within 4Å: Chain A: R.254 Chain C: H.69, V.73, F.104, G.105, H.144, R.145, V.146, R.155, N.193, V.194, D.195, F.230, R.234 Ligands: COA.5 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.73, C:F.104 Hydrogen bonds: C:G.105, C:H.144, C:R.155, C:R.155 Water bridges: C:H.144, C:R.234 Salt bridges: C:H.69, C:H.69, C:H.144, C:R.155, C:R.234, A:R.254

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

PEG.3: 8 residues within 4Å: Chain A: Q.57, E.60, M.61, M.64, Y.162 Chain B: F.32, E.35, G.37 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:G.37 Hydrogen bonds: A:Q.57, A:E.60

1 x CAO: OXIDIZED COENZYME A(Non-covalent)

CAO.4: 18 residues within 4Å: Chain B: D.102, R.103, G.106, A.107, A.110, K.133, L.138, I.139, M.140, G.141, I.142, G.143, H.144, R.145, K.187, N.189, L.190, N.193 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.102, B:K.133, B:I.139, B:I.139, B:G.141, B:I.142, B:N.189 Water bridges: B:G.106 Salt bridges: B:K.133, B:K.187, B:K.187

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

EDO.8: 7 residues within 4Å: Chain C: F.32, G.37, I.38 Chain D: Q.57, E.60, M.61, M.64 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.57 Water bridges: D:E.60, C:G.37

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
E

B
F

C
G

D
H

ATP-citrate synthase

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