SMTL ID : 6qfb.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 3.25 Å

Oligo State

homo-tetramer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 16 residues within 4Å: Chain A: K.904, L.909, I.910, I.913, K.957, K.958, L.961 Chain C: F.473, F.512, A.513, S.514, R.516, S.517, I.537, E.539, A.564 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:I.910, A:I.910, C:S.514, C:S.517, C:I.537 Salt bridges: A:K.904, A:K.957, A:K.958, A:K.958, C:R.516 Hydrophobic interactions: C:E.539 COA.5: 15 residues within 4Å: Chain B: K.904, L.909, I.910, I.913, K.957, K.958, L.961 Chain D: F.473, F.512, A.513, S.514, R.516, S.517, I.537, E.539 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:I.910, B:I.910, D:S.514, D:S.517 Salt bridges: B:K.904, B:K.957, B:K.958, B:K.958, D:R.516 Hydrophobic interactions: D:F.512, D:E.539 COA.8: 16 residues within 4Å: Chain A: F.473, F.512, A.513, S.514, R.516, S.517, I.537, E.539, A.564 Chain C: K.904, L.909, I.910, I.913, K.957, K.958, L.961 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:E.539 Hydrogen bonds: A:S.514, A:S.517, A:I.537, C:I.910, C:I.910 Salt bridges: A:R.516, C:K.904, C:K.957, C:K.958, C:K.958 COA.12: 15 residues within 4Å: Chain B: F.473, F.512, A.513, S.514, R.516, S.517, I.537, E.539 Chain D: K.904, L.909, I.910, I.913, K.957, K.958, L.961 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:F.512, B:E.539 Hydrogen bonds: B:S.514, B:S.517, D:I.910, D:I.910 Salt bridges: B:R.516, D:K.904, D:K.957, D:K.958, D:K.958

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

ADP.2: 16 residues within 4Å: Chain A: 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.3 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.6: 18 residues within 4Å: Chain B: V.56, K.58, R.65, R.66, G.67, 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.7 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.9: 16 residues within 4Å: Chain C: 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.10 10 PLIP interactions: 10 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 Salt bridges: C:K.58, C:R.66, C:R.66 ADP.13: 18 residues within 4Å: Chain D: V.56, K.58, R.65, R.66, G.67, 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.14 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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.203, P.204, D.216 Ligands: ADP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.203, A:D.216 MG.7: 4 residues within 4Å: Chain B: G.139, N.203, D.216 Ligands: ADP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:N.203, B:D.216 MG.10: 4 residues within 4Å: Chain C: N.203, P.204, D.216 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:N.203, C:D.216 MG.14: 4 residues within 4Å: Chain D: G.139, N.203, D.216 Ligands: ADP.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:N.203, D:D.216

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

2HP.4: 5 residues within 4Å: Chain B: G.282, G.283, S.603, G.604, G.605 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.282, B:G.283, B:G.604, B:G.605 2HP.11: 5 residues within 4Å: Chain D: G.282, G.283, S.603, G.604, G.605 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.282, D:G.283, D:G.604, D:G.605

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
C

B
D

C
C

D
D

ATP-citrate synthase

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