SMTL ID : 8g5c.1

Structure of ACLY-D1026A-substrates, local refinement of ASH domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

ADP.1: 15 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 13 PLIP interactions: 13 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:V.140, A:D.216, A:D.216 Salt bridges: A:K.58, A:R.66, A:R.66

4 x COA: COENZYME A(Non-covalent)

COA.2: 17 residues within 4Å: Chain A: A.903, A.938, L.969, I.970, M.971, G.972, I.973, G.974, H.975, R.976, N.1024, A.1026 Chain B: R.1085, H.1086, P.1087, W.1088 Ligands: FLC.3 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.1085, B:R.1085, B:W.1088, A:G.972, A:I.973, A:R.976, A:N.1024 pi-Stacking: B:W.1088, B:W.1088, B:W.1088 COA.6: 17 residues within 4Å: Chain A: R.1085, H.1086, P.1087, W.1088 Chain B: A.903, A.938, L.969, I.970, M.971, G.972, I.973, G.974, R.976, N.1020, N.1024, A.1026 Ligands: FLC.7 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.1085, A:H.1086, A:W.1088, B:G.972, B:I.973, B:R.976, B:R.976, B:N.1020, B:N.1024 pi-Stacking: A:W.1088, A:W.1088 COA.8: 17 residues within 4Å: Chain C: A.903, A.938, I.970, M.971, G.972, I.973, G.974, H.975, R.976, N.1024, V.1025, A.1026 Chain D: R.1085, H.1086, P.1087, W.1088 Ligands: Q5B.5 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.972, C:I.973, C:R.976, C:N.1024, D:H.1086, D:W.1088 pi-Stacking: D:W.1088, D:W.1088, D:W.1088 COA.10: 18 residues within 4Å: Chain C: R.1085, H.1086, P.1087, W.1088 Chain D: A.903, A.938, L.969, I.970, M.971, G.972, I.973, G.974, H.975, R.976, N.1020, N.1024, A.1026 Ligands: FLC.11 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:G.972, D:I.973, D:R.976, D:N.1020, D:N.1024, C:R.1085, C:R.1085, C:W.1088 pi-Stacking: C:W.1088, C:W.1088, C:W.1088

4 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 9 residues within 4Å: Chain A: H.900, V.904, F.935, G.936, R.986, F.1061, R.1065 Chain B: R.1085 Ligands: COA.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.900, A:F.935, A:F.1061 Hydrogen bonds: A:H.900, A:G.936, A:R.1065, A:R.1065 Salt bridges: A:H.900, A:H.900, A:R.986, B:R.1085 FLC.7: 8 residues within 4Å: Chain A: R.1085 Chain B: H.900, V.904, F.935, G.936, F.1061, R.1065 Ligands: COA.6 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.935, B:F.1061 Hydrogen bonds: B:H.900, B:G.936, B:R.1065, B:R.1065 Salt bridges: B:H.900, B:H.900, B:R.986, B:R.1065, A:R.1085 FLC.9: 6 residues within 4Å: Chain C: H.900, V.904, F.935, G.936, F.1061, R.1065 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.935, C:F.1061 Hydrogen bonds: C:H.900, C:G.936, C:R.1065 Salt bridges: C:H.900, C:H.900, C:R.986, C:R.1065, D:R.1085 FLC.11: 10 residues within 4Å: Chain C: R.1085 Chain D: H.900, V.904, F.935, G.936, R.986, V.1025, F.1061, R.1065 Ligands: COA.10 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.904, D:F.935 Hydrogen bonds: D:G.936, D:R.1065, D:R.1065 Salt bridges: D:H.900, D:H.900, D:R.986, D:R.1065, C:R.1085

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

PO4.4: 8 residues within 4Å: Chain A: G.281, G.282, G.283, S.308, S.663, G.664, G.665 Ligands: Q5B.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.282, A:G.283, A:S.308, A:S.308, A:G.664, A:G.665

1 x Q5B: (3S)-citryl-Coenzyme A(Non-covalent)

Q5B.5: 29 residues within 4Å: Chain A: S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, Q.505, F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, V.626, N.638, G.665 Chain C: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: PO4.4, COA.8 26 PLIP interactions: 20 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.572, A:I.597 Hydrogen bonds: A:S.308, A:G.309, A:S.343, A:N.346, A:N.346, A:F.347, A:T.348, A:T.348, A:S.574, A:S.577, A:S.577, A:S.577, A:N.638, C:I.970, C:I.970 Water bridges: A:I.597, A:T.625, A:N.638 Salt bridges: A:R.379, A:R.576, C:K.964, C:K.1017, C:K.1018, C:K.1018

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, X. et al., Allosteric role of the citrate synthase homology domain of ATP citrate lyase. Nat Commun (2023)

Release Date

2023-05-10

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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