SMTL ID : 8g5d.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

ACO.1: 17 residues within 4Å: Chain A: 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 B: R.1085, H.1086, P.1087, W.1088 Ligands: OAA.2 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.1026 Hydrogen bonds: A:G.972, A:I.973, A:I.973, A:R.976, A:N.1024, A:V.1025, A:A.1026, B:R.1085, B:H.1086, B:W.1088 pi-Stacking: B:W.1088, B:W.1088, B:W.1088 ACO.3: 19 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, H.975, R.976, N.1024, V.1025, A.1026 Ligands: OAA.4, Q5B.9 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.1026 Hydrogen bonds: B:G.972, B:I.973, B:I.973, B:R.976, B:N.1024, B:V.1025, B:A.1026, A:R.1085, A:H.1086, A:W.1088 pi-Stacking: A:W.1088, A:W.1088 ACO.5: 19 residues within 4Å: Chain C: A.903, A.938, L.969, I.970, M.971, G.972, I.973, G.974, H.975, R.976, N.1020, N.1024, V.1025, A.1026 Chain D: R.1085, H.1086, P.1087, W.1088 Ligands: OAA.6 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:R.1085, D:H.1086, D:W.1088, C:G.972, C:I.973, C:I.973, C:N.1024, C:A.1026 pi-Stacking: D:W.1088, D:W.1088, D:W.1088 Hydrophobic interactions: C:A.938, C:A.1026 ACO.7: 20 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, V.977, N.1020, N.1024, V.1025, A.1026 Ligands: OAA.8 14 PLIP interactions: 6 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:R.1085, C:H.1086, C:W.1088, D:G.972, D:I.973, D:I.973, D:R.976, D:N.1020, D:V.1025, D:A.1026 pi-Stacking: C:W.1088, C:W.1088, C:W.1088 Hydrophobic interactions: D:A.1026

4 x OAA: OXALOACETATE ION(Non-covalent)

OAA.2: 7 residues within 4Å: Chain A: H.900, V.904, F.935, R.986, R.1065 Chain B: R.1085 Ligands: ACO.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.900, B:R.1085 Salt bridges: A:H.900, A:R.986, A:R.1065 OAA.4: 6 residues within 4Å: Chain B: H.900, V.904, F.935, R.986, R.1065 Ligands: ACO.3 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.900, B:R.986, B:R.1065 Hydrogen bonds: A:R.1085 OAA.6: 7 residues within 4Å: Chain C: H.900, V.904, F.935, R.986, F.1061, R.1065 Ligands: ACO.5 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:H.900, C:R.986, C:R.1065 OAA.8: 7 residues within 4Å: Chain C: R.1085 Chain D: H.900, V.904, F.935, R.986, R.1065 Ligands: ACO.7 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.900, C:R.1085 Salt bridges: D:H.900, D:R.986, D:R.1065

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

Q5B.9: 31 residues within 4Å: Chain B: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain D: G.261, A.280, S.308, G.309, 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, E.599, A.624, T.625, V.626, G.665 Ligands: ACO.3, PO4.11 22 PLIP interactions: 16 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:F.572, D:I.597 Hydrogen bonds: D:G.309, D:A.310, D:N.346, D:N.346, D:F.347, D:T.348, D:T.348, D:S.574, D:S.577, D:S.577, D:S.577, D:I.597, B:I.970, B:I.970 Salt bridges: D:R.379, D:R.576, B:K.964, B:K.1017, B:K.1018, B:K.1018

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

ADP.10: 14 residues within 4Å: Chain D: V.56, K.58, R.65, R.66, G.67, P.109, F.110, V.111, H.113, V.140, N.203, P.204, L.215, D.216 12 PLIP interactions: 12 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:H.113, D:D.216 Salt bridges: D:K.58, D:R.65, D:R.66, D:R.66

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

PO4.11: 8 residues within 4Å: Chain D: G.282, G.283, S.308, A.624, S.663, G.664, H.760 Ligands: Q5B.9 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.282, D:G.283, D:S.308, D:G.664, D:G.665 Salt bridges: D:H.760

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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