SMTL ID : 7rkz.1

Structure of ACLY D1026A-substrates-asym-int

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

3 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, V.72, V.74, P.109, F.110, H.113, V.140, N.203, P.204, L.215, D.216 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.58, A:R.66, A:G.67, A:P.109, A:H.113 Salt bridges: A:R.65, A:R.65, A:R.66 ADP.6: 16 residues within 4Å: Chain B: V.56, K.58, I.63, K.64, R.65, R.66, G.67, V.72, P.109, F.110, V.111, H.113, V.140, P.204, L.215, D.216 10 PLIP interactions: 10 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:D.216 Salt bridges: B:R.66, B:R.66 pi-Cation interactions: B:H.113 ADP.14: 15 residues within 4Å: Chain D: V.56, K.58, R.65, R.66, G.67, V.72, E.108, P.109, F.110, H.113, E.118, N.203, P.204, L.215, D.216 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.58, D:R.66, D:G.67, D:E.108, D:P.109, D:V.111, D:E.118, D:N.203, D:D.216 Salt bridges: D:R.65, D:R.66

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

Q5B.2: 27 residues within 4Å: Chain A: 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, 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: COA.10 23 PLIP interactions: 17 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.572, A:F.572 Hydrogen bonds: A:G.309, A:N.346, A:N.346, A:F.347, A:T.348, A:S.574, A:R.576, A:S.577, A:S.577, A:S.577, A:N.638, C:I.970, C:I.970 Water bridges: A:S.574, A:S.574 Salt bridges: A:R.379, A:R.576, C:K.964, C:K.1017, C:K.1018, C:K.1018 Q5B.7: 28 residues within 4Å: Chain B: A.280, 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, E.599, V.626, N.638 Chain D: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: COA.11 25 PLIP interactions: 19 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:F.572, B:I.597 Hydrogen bonds: B:G.309, B:S.343, B:S.343, B:N.346, B:N.346, B:F.347, B:T.348, B:T.348, B:S.574, B:S.577, B:S.577, B:N.638, D:I.970, D:I.970 Water bridges: B:S.574, B:S.574, B:N.638 Salt bridges: B:R.379, B:R.576, D:K.964, D:K.1017, D:K.1018, D:K.1018 Q5B.15: 28 residues within 4Å: Chain B: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain D: G.281, S.308, G.309, N.346, F.347, T.348, Q.505, F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, T.625, V.626, N.638, G.664, G.665 Ligands: COA.9 22 PLIP interactions: 16 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:I.597 Hydrogen bonds: D:S.308, D:G.309, D:S.343, D:N.346, D:N.346, D:F.347, D:T.348, D:T.348, D:S.574, D:S.574, D:S.577, D:S.577, D:E.599, 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

4 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 7 residues within 4Å: Chain A: H.900, V.904, F.935, G.936, R.986, R.1065 Ligands: COA.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.900 Hydrogen bonds: A:G.936 Water bridges: A:G.937 Salt bridges: A:H.900, A:H.900, A:R.986, A:R.1065 FLC.8: 9 residues within 4Å: Chain B: H.900, V.904, F.935, G.936, A.938, R.986, F.1061, R.1065 Ligands: COA.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.900, B:F.1061 Hydrogen bonds: B:G.936, B:R.1065 Water bridges: B:A.938, B:A.938 Salt bridges: B:H.900, B:H.900, B:R.986, B:R.1065 FLC.12: 8 residues within 4Å: Chain C: H.900, V.904, F.935, G.936, A.938, F.1061, R.1065 Ligands: COA.10 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:H.900, C:F.935, C:F.1061 Hydrogen bonds: C:H.900, C:G.936, C:R.1065, C:R.1065 Water bridges: C:A.938 Salt bridges: C:H.900, C:R.986, C:R.1065 FLC.16: 11 residues within 4Å: Chain C: R.1085 Chain D: H.900, V.904, F.935, G.936, A.938, R.986, V.1025, F.1061, R.1065 Ligands: COA.11 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:H.900, D:F.1061 Hydrogen bonds: D:G.936, D:R.1065, C:R.1085 Salt bridges: D:H.900, D:H.900, D:R.986, D:R.1065

2 x UNL: UNKNOWN LIGAND

UNL.4: 2 residues within 4Å: Chain A: M.823 Chain B: L.833 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.833 UNL.13: 2 residues within 4Å: Chain C: M.823 Chain D: L.833 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.833

4 x COA: COENZYME A(Non-covalent)

COA.5: 15 residues within 4Å: Chain A: A.938, L.969, I.970, M.971, G.972, I.973, G.974, R.976, K.1018, N.1020, L.1021, N.1024, A.1026 Chain C: F.533 Ligands: FLC.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.970, A:I.970, A:G.972, A:I.973, A:I.973, A:K.1018, A:N.1020, A:N.1020 Salt bridges: A:R.976, A:K.1018 COA.9: 18 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, V.977, N.1024 Ligands: FLC.8, Q5B.15 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.1085, A:R.1085, A:H.1086, A:W.1088, B:G.972, B:I.973, B:N.1024 Salt bridges: A:R.1085 pi-Stacking: A:W.1088, A:W.1088, A:W.1088 pi-Cation interactions: A:R.1085 COA.10: 16 residues within 4Å: Chain C: A.903, A.938, L.969, I.970, M.971, G.972, I.973, G.974, R.976, N.1024 Chain D: R.1085, H.1086, P.1087, W.1088 Ligands: Q5B.2, FLC.12 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:G.972, C:I.973, C:R.976, C:R.976, C:N.1024, D:R.1085, D:W.1088 Water bridges: D:D.1089 pi-Stacking: D:W.1088, D:W.1088, D:W.1088 COA.11: 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.1024, A.1026 Ligands: Q5B.7, FLC.16 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.1085, C:W.1088, D:G.972, D:I.973, D:R.976, D:N.1024 pi-Stacking: C:W.1088, C:W.1088, C:W.1088

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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