SMTL ID : 6qfb.1 (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 3.25 Å

Oligo State

homo-tetramer

Ligands

4 x 2HP: DIHYDROGENPHOSPHATE ION(Non-covalent)

2HP.1: 5 residues within 4Å: Chain A: G.282, G.283, S.603, G.604, G.605 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.282, A:G.283, A:G.604, A:G.605 2HP.5: 10 residues within 4Å: Chain B: G.281, G.282, G.283, S.308, S.603, G.604, G.605 Ligands: COA.2, FLC.6, MG.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.282, B:G.283, B:S.308, B:G.604, B:G.605 2HP.11: 5 residues within 4Å: Chain C: G.282, G.283, S.603, G.604, G.605 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.282, C:G.283, C:G.604, C:G.605 2HP.15: 10 residues within 4Å: Chain D: G.281, G.282, G.283, S.308, S.603, G.604, G.605 Ligands: COA.12, FLC.16, MG.20 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.282, D:G.283, D:S.308, D:G.604, D:G.605

4 x COA: COENZYME A(Non-covalent)

COA.2: 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, A.513, S.514, R.516, S.517, I.537, E.539, A.564, T.565, V.566 Ligands: 2HP.5, FLC.6 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:I.910, A:I.910, B:G.261, B:S.514, B:S.517, B:I.537, B:E.539 Salt bridges: A:K.904, A:K.957, A:K.958, A:K.958, B:R.516 Hydrophobic interactions: B:E.539 COA.7: 14 residues within 4Å: Chain A: F.473, F.512, A.513, S.514, R.516, S.517, E.539 Chain B: K.904, L.909, I.910, I.913, K.957, K.958, L.961 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:I.910, B:I.910, A:S.514, A:S.517, A:E.539 Salt bridges: B:K.904, B:K.957, B:K.958, B:K.958, A:R.516 COA.12: 23 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 Ligands: 2HP.15, FLC.16 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 COA.17: 14 residues within 4Å: Chain C: F.473, F.512, A.513, S.514, R.516, S.517, E.539 Chain D: K.904, L.909, I.910, I.913, K.957, K.958, L.961 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:I.910, D:I.910, C:S.514, C:S.517, C:E.539 Salt bridges: D:K.904, D:K.957, D:K.958, D:K.958, C:R.516

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

ADP.3: 18 residues within 4Å: Chain A: V.56, K.58, 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.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.58, A:R.65, A:R.66, A:G.67, A:P.109, A:V.111, A:E.118, A:D.216 Salt bridges: A:K.58, A:R.66, A:R.66 ADP.8: 16 residues within 4Å: Chain B: V.56, K.58, R.65, R.66, G.67, P.109, F.110, V.111, H.113, E.118, V.140, N.203, P.204, L.215, D.216 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.58, B:R.65, B:R.66, B:G.67, B:P.109, B:V.111, B:E.118, B:D.216 Salt bridges: B:K.58, B:R.66, B:R.66 ADP.13: 18 residues within 4Å: Chain C: V.56, K.58, 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.14 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.58, C:R.65, C:R.66, C:G.67, C:P.109, C:V.111, C:E.118, C:D.216, C:D.216 Salt bridges: C:K.58, C:R.66, C:R.66 ADP.18: 16 residues within 4Å: Chain D: V.56, K.58, R.65, R.66, G.67, P.109, F.110, V.111, H.113, E.118, V.140, N.203, P.204, L.215, D.216 Ligands: MG.19 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.58, D:R.65, D:R.66, D:G.67, D:P.109, D:V.111, D:E.118 Salt bridges: D:K.58, D:R.66, D:R.66

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: N.203, D.216 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.203, A:D.216 MG.9: 3 residues within 4Å: Chain B: N.203, D.216 Ligands: ADP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:N.203, B:D.216 MG.10: 4 residues within 4Å: Chain B: S.308, E.539 Ligands: 2HP.5, FLC.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.308 MG.14: 3 residues within 4Å: Chain C: N.203, D.216 Ligands: ADP.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:N.203, C:D.216 MG.19: 3 residues within 4Å: Chain D: N.203, D.216 Ligands: ADP.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:N.203, D:D.216 MG.20: 4 residues within 4Å: Chain D: S.308, E.539 Ligands: 2HP.15, FLC.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.308

2 x FLC: CITRATE ANION(Non-covalent)

FLC.6: 13 residues within 4Å: Chain B: A.280, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, G.605 Ligands: COA.2, 2HP.5, MG.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.308, B:G.309, B:S.343, B:N.346, B:F.347, B:T.348, B:T.348, B:T.348 Salt bridges: B:R.379 FLC.16: 13 residues within 4Å: Chain D: A.280, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, G.605 Ligands: COA.12, 2HP.15, MG.20 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.308, D:G.309, D:S.343, D:N.346, D:F.347, D:T.348, D:T.348, D:T.348 Salt bridges: D:R.379

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
A

D
B

ATP-citrate synthase

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