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

Structure of the human ATP citrate lyase holoenzyme in complex with citrate, coenzyme A and Mg.ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.306, S.308, E.539 Ligands: PO4.2, FLC.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.308 MG.6: 3 residues within 4Å: Chain A: N.203, D.216 Ligands: ADP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.203, A:D.216, H2O.1 MG.7: 4 residues within 4Å: Chain B: S.308, E.539 Ligands: PO4.8, FLC.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.308 MG.12: 3 residues within 4Å: Chain B: N.203, D.216 Ligands: ADP.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.203, B:D.216, H2O.1 MG.13: 4 residues within 4Å: Chain C: S.308, E.539 Ligands: PO4.14, FLC.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.308, C:E.539, C:E.539 MG.18: 3 residues within 4Å: Chain C: N.203, D.216 Ligands: ADP.17 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.203, C:D.216, H2O.1, H2O.1 MG.19: 5 residues within 4Å: Chain D: E.306, S.308, E.539 Ligands: PO4.20, FLC.21 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.308, D:E.539, D:E.539 MG.24: 3 residues within 4Å: Chain D: N.203, D.216 Ligands: ADP.23 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:N.203, D:D.216, H2O.1, H2O.1

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 11 residues within 4Å: Chain A: G.281, G.282, G.283, S.308, S.603, G.604, G.605, H.700 Ligands: MG.1, FLC.3, COA.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.282, A:G.283, A:G.604, A:G.605 Salt bridges: A:H.700 PO4.8: 11 residues within 4Å: Chain B: G.281, G.282, G.283, S.308, S.603, G.604, G.605, H.700 Ligands: MG.7, FLC.9, COA.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.282, B:G.283, B:G.604, B:G.605 Salt bridges: B:H.700 PO4.14: 11 residues within 4Å: Chain C: G.281, G.282, G.283, S.308, S.603, G.604, G.605, H.700 Ligands: MG.13, FLC.15, COA.16 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.282, C:G.283, C:A.284, C:G.604, C:G.605 Salt bridges: C:H.700 PO4.20: 11 residues within 4Å: Chain D: G.281, G.282, G.283, S.308, S.603, G.604, G.605, H.700 Ligands: MG.19, FLC.21, COA.22 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.282, D:G.283, D:S.308, D:S.603, D:S.603, D:G.604, D:G.605 Salt bridges: D:H.700

4 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 14 residues within 4Å: Chain A: G.281, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, G.604, G.605 Ligands: MG.1, PO4.2, COA.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.347 Hydrogen bonds: A:G.309, A:N.346, A:N.346, A:F.347, A:T.348, A:T.348, A:T.348, A:T.348, A:T.348 Salt bridges: A:R.379 FLC.9: 15 residues within 4Å: Chain B: A.280, G.281, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, G.604, G.605 Ligands: MG.7, PO4.8, COA.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.347 Hydrogen bonds: B:G.309, B:A.310, B:S.343, B:N.346, B:N.346, B:F.347, B:T.348, B:T.348 Salt bridges: B:R.379 FLC.15: 14 residues within 4Å: Chain C: A.280, G.281, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, G.605 Ligands: MG.13, PO4.14, COA.16 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.347 Hydrogen bonds: C:G.309, C:N.346, C:N.346, C:F.347, C:T.348, C:T.348, C:T.348, C:T.348, C:T.348 Salt bridges: C:R.379 FLC.21: 15 residues within 4Å: Chain D: A.280, G.281, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, G.604, G.605 Ligands: MG.19, PO4.20, COA.22 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.308, D:G.309, D:N.346, D:N.346, D:F.347, D:T.348, D:T.348, D:T.348, D:T.348 Salt bridges: D:R.379

4 x COA: COENZYME A(Non-covalent)

COA.4: 24 residues within 4Å: Chain A: G.261, G.309, F.347, F.473, F.512, A.513, S.514, R.516, S.517, I.537, E.539, A.564, T.565, V.566, G.604 Chain B: K.904, L.909, I.910, I.913, K.957, K.958, L.961 Ligands: PO4.2, FLC.3 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.512, A:E.539 Hydrogen bonds: A:G.261, A:S.514, A:S.517, A:I.537, B:I.910, B:I.910 Salt bridges: A:R.516, B:K.904, B:K.957, B:K.958, B:K.958 COA.10: 23 residues within 4Å: Chain A: K.904, L.909, I.910, I.913, K.957, K.958, L.961 Chain B: G.261, G.309, F.347, F.473, F.512, S.514, R.516, S.517, I.537, E.539, A.564, T.565, V.566, G.604 Ligands: PO4.8, FLC.9 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:I.910, A:I.910, B:G.261, B:S.514, B:S.517, B:I.537 Salt bridges: A:K.904, A:K.957, A:K.958, A:K.958, B:R.516 Hydrophobic interactions: B:E.539 COA.16: 23 residues within 4Å: Chain C: G.261, F.347, F.473, F.512, A.513, S.514, R.516, S.517, I.537, E.539, A.564, T.565, V.566, G.604 Chain D: K.904, L.909, I.910, I.913, K.957, K.958, L.961 Ligands: PO4.14, FLC.15 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:I.910, D:I.910, C:G.261, C:S.514, C:I.537 Salt bridges: D:K.904, D:K.957, D:K.958, D:K.958, C:R.516 Hydrophobic interactions: C:E.539 COA.22: 24 residues within 4Å: Chain C: K.904, L.909, I.910, I.913, K.957, K.958, L.961 Chain D: G.261, G.309, F.347, F.473, F.512, A.513, S.514, R.516, S.517, I.537, E.539, A.564, T.565, V.566, G.604 Ligands: PO4.20, FLC.21 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:I.910, C:I.910, D:G.261, D:S.514, D:S.517, D:I.537 Salt bridges: C:K.904, C:K.957, C:K.958, C:K.958, D:R.516 Hydrophobic interactions: D:E.539

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 21 residues within 4Å: Chain A: V.56, K.58, I.63, K.64, R.65, R.66, G.67, K.68, V.72, P.109, F.110, V.111, H.113, E.118, G.139, V.140, N.203, P.204, L.215, D.216 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.58, A:R.66, A:G.67, A:P.109, A:V.111, A:E.118, A:V.140, A:N.203, A:D.216 Water bridges: A:R.66, A:R.66, A:G.139, A:N.203 Salt bridges: A:K.58, A:R.66, A:R.66 ADP.11: 21 residues within 4Å: Chain B: V.56, K.58, I.63, K.64, R.65, R.66, G.67, V.72, E.108, P.109, F.110, V.111, H.113, E.118, G.139, V.140, N.203, P.204, L.215, D.216 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:I.63, B:R.66, B:G.67, B:P.109, B:V.111, B:E.118 Water bridges: B:G.139, B:N.203, B:N.203 Salt bridges: B:R.66, B:R.66 ADP.17: 21 residues within 4Å: Chain C: V.56, K.58, I.63, K.64, R.65, R.66, G.67, V.72, V.74, P.109, F.110, V.111, H.113, E.118, G.139, V.140, N.203, P.204, L.215, D.216 Ligands: MG.18 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:K.58, C:R.66, C:G.67, C:P.109, C:V.111, C:E.118, C:E.118, C:V.140 Water bridges: C:N.203, C:N.203 Salt bridges: C:K.58, C:R.66, C:R.66 ADP.23: 20 residues within 4Å: Chain D: V.56, K.58, I.63, K.64, R.65, R.66, G.67, V.72, P.109, F.110, V.111, H.113, E.118, G.139, V.140, N.203, P.204, L.215, D.216 Ligands: MG.24 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:K.58, D:K.64, D:R.66, D:G.67, D:P.109, D:V.111, D:E.118, D:N.203, D:D.216 Water bridges: D:G.139, D:P.204 Salt bridges: D:K.58, D:R.66, D:R.66

Links

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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,Human ATP citrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

ATP-citrate synthase,Human ATP citrate lyase

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