SMTL ID : 7lla.1

Structure of human ATP citrate lyase in complex with acetyl-CoA and oxaloacetate (EM map was generated in Cryosparc with non-uniform refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 18 residues within 4Å: Chain A: F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, E.599, T.625 Chain C: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: OAA.2 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:I.970, C:I.970, A:S.574, A:S.577, A:E.599 Salt bridges: C:K.964, C:K.1017, C:K.1018, C:K.1018, A:R.576 Hydrophobic interactions: A:A.598, A:E.599 ACO.5: 19 residues within 4Å: Chain B: F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, E.599, A.624, T.625 Chain D: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: OAA.6 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:A.598 Hydrogen bonds: B:S.574, B:S.574, B:E.599, D:I.970, D:I.970 Salt bridges: B:R.576, D:K.964, D:K.1017, D:K.1018 ACO.8: 19 residues within 4Å: Chain A: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain C: F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, E.599, A.624, T.625 Ligands: OAA.9 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.598, C:E.599 Hydrogen bonds: C:S.574, C:S.574, C:S.577, C:E.599, A:I.970, A:I.970 Salt bridges: C:R.576, A:K.964, A:K.1017, A:K.1018, A:K.1018 ACO.11: 19 residues within 4Å: Chain B: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain D: F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, E.599, A.624, T.625 Ligands: OAA.12 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:A.598 Hydrogen bonds: D:S.574, D:S.574, D:E.599, B:I.970, B:I.970 Salt bridges: D:R.576, B:K.964, B:K.1017, B:K.1018

8 x OAA: OXALOACETATE ION(Non-covalent)

OAA.2: 7 residues within 4Å: Chain A: G.309, A.310, N.346, F.347, T.348, N.638 Ligands: ACO.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.309, A:N.346, A:T.348, A:T.348, A:N.638 OAA.3: 8 residues within 4Å: Chain A: H.900, V.904, F.935, G.936, D.1026, F.1061, R.1065 Chain B: R.1085 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Salt bridges: B:R.1085, A:H.900 Hydrophobic interactions: A:F.935 Hydrogen bonds: A:G.936, A:R.1065, A:R.1065 OAA.4: 7 residues within 4Å: Chain A: R.1085 Chain B: H.900, F.935, G.936, D.1026, F.1061, R.1065 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.935 Hydrogen bonds: B:G.936, B:R.1065, B:R.1065 Salt bridges: B:H.900, A:R.1085 OAA.6: 6 residues within 4Å: Chain B: G.309, N.346, F.347, T.348, N.638 Ligands: ACO.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.348, B:T.348, B:N.638 OAA.7: 8 residues within 4Å: Chain C: H.900, V.904, F.935, G.936, D.1026, F.1061, R.1065 Chain D: R.1085 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.935 Hydrogen bonds: C:G.936, C:R.1065, C:R.1065 Salt bridges: C:H.900, D:R.1085 OAA.9: 7 residues within 4Å: Chain C: G.309, A.310, N.346, F.347, T.348, N.638 Ligands: ACO.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.309, C:N.346, C:T.348, C:T.348, C:N.638 OAA.10: 8 residues within 4Å: Chain C: R.1085 Chain D: H.900, R.934, F.935, G.936, D.1026, F.1061, R.1065 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.935 Hydrogen bonds: D:G.936, D:D.1026, D:R.1065, D:R.1065 Salt bridges: D:H.900, C:R.1085 OAA.12: 7 residues within 4Å: Chain D: G.309, A.310, N.346, F.347, T.348, N.638 Ligands: ACO.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.309, D:N.346, D:T.348, D:T.348, D:N.638

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, X. et al., Reply to: Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-03-03

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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