SMTL ID : 7rig.1

Structure of ACLY-D1026A-substrates

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: V.56, K.58, K.64, R.65, R.66, G.67, V.74, E.108, P.109, F.110, V.111, H.113, E.118, N.203, P.204, L.215, D.216 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.66, A:G.67, A:P.109, A:V.111, A:H.113, A:D.216, A:D.216 Salt bridges: A:K.58, A:R.66, A:R.66 ADP.7: 16 residues within 4Å: Chain B: V.56, K.58, R.65, R.66, G.67, V.74, E.108, P.109, F.110, V.111, H.113, E.118, N.203, P.204, L.215, D.216 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.58, B:R.65, B:R.66, B:R.66, B:G.67, B:P.109, B:V.111, B:H.113, B:D.216 Salt bridges: B:K.58, B:R.66 ADP.13: 16 residues within 4Å: Chain C: V.56, K.58, R.65, R.66, G.67, V.74, E.108, P.109, F.110, V.111, H.113, E.118, N.203, P.204, L.215, D.216 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.58, C:R.65, C:R.66, C:R.66, C:G.67, C:P.109, C:V.111, C:H.113, C:D.216 Salt bridges: C:K.58, C:R.66 ADP.19: 17 residues within 4Å: Chain D: V.56, K.58, K.64, R.65, R.66, G.67, V.74, E.108, P.109, F.110, V.111, H.113, E.118, N.203, P.204, L.215, D.216 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.66, D:G.67, D:P.109, D:V.111, D:H.113, D:D.216, D:D.216 Salt bridges: D:K.58, D:R.66, D:R.66

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

Q5B.2: 26 residues within 4Å: Chain A: 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 Chain C: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: PO4.6, COA.12 28 PLIP interactions: 22 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.572, A:F.572, A:I.597 Hydrogen bonds: A:G.309, A:A.310, A:N.346, A:N.346, A:F.347, A:T.348, 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, A:E.599, A:N.638 Salt bridges: A:R.379, A:R.576, C:K.964, C:K.1017, C:K.1018, C:K.1018 Q5B.8: 26 residues within 4Å: Chain B: 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 Chain D: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: PO4.11, COA.17 27 PLIP interactions: 21 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:F.572, B:F.572, B:I.597 Hydrogen bonds: B:G.309, 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:S.577, B:N.638, D:I.970, D:I.970 Water bridges: B:S.574, B:S.574, B:I.597, B:T.625, B:N.638 Salt bridges: B:R.379, B:R.576, D:K.964, D:K.1017, D:K.1018, D:K.1018 Q5B.14: 27 residues within 4Å: Chain A: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain C: 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 Ligands: COA.5, PO4.16 26 PLIP interactions: 20 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:F.572, C:F.572, C:I.597 Hydrogen bonds: C:G.309, C:A.310, C:N.346, C:N.346, C:F.347, C:T.348, C:T.348, C:S.574, C:S.577, C:S.577, C:S.577, C:N.638, A:I.970, A:I.970 Water bridges: C:S.574, C:S.574, C:N.638 Salt bridges: C:R.379, C:R.576, A:K.964, A:K.1017, A:K.1018, A:K.1018 Q5B.20: 27 residues within 4Å: Chain B: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain D: G.281, 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 Ligands: COA.10, PO4.22 29 PLIP interactions: 23 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:F.572, 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:R.576, D:S.577, D:S.577, D:S.577, D:N.638, B:I.970, B:I.970 Water bridges: D:S.574, D:S.574, D:I.597, D:T.625, D:N.638 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: 8 residues within 4Å: Chain A: H.900, V.904, F.935, G.936, R.986, F.1061, R.1065 Chain B: R.1085 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Salt bridges: B:R.1085, A:H.900, A:H.900, A:R.986, A:R.1065 Hydrophobic interactions: A:V.904, A:F.935 Hydrogen bonds: A:G.936, A:R.1065, A:R.1065 Water bridges: A:R.986, A:R.986 FLC.9: 8 residues within 4Å: Chain B: H.900, V.904, F.935, G.936, R.986, F.1061, R.1065 Ligands: COA.10 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.904, B:F.935 Hydrogen bonds: B:G.936, B:R.1065, B:R.1065 Water bridges: B:A.938, B:R.986 Salt bridges: B:H.900, B:R.986, B:R.1065, A:R.1085 FLC.15: 8 residues within 4Å: Chain C: H.900, V.904, F.935, G.936, R.986, F.1061, R.1065 Chain D: R.1085 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.904, C:F.935 Hydrogen bonds: C:G.936, C:R.1065, C:R.1065 Water bridges: C:R.986 Salt bridges: C:H.900, C:H.900, C:R.986, C:R.1065, D:R.1085 FLC.21: 8 residues within 4Å: Chain C: R.1085 Chain D: H.900, V.904, F.935, G.936, R.986, F.1061, R.1065 11 PLIP interactions: 10 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 Water bridges: D:R.986 Salt bridges: D:H.900, D:H.900, D:R.986, D:R.1065, C:R.1085

2 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x COA: COENZYME A(Non-covalent)

COA.5: 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: Q5B.14 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.1085, B:R.1085, B:W.1088, A:G.972, A:I.973, A:N.1024 Water bridges: B:D.1089 pi-Stacking: B:W.1088, B:W.1088, B:W.1088 COA.10: 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, N.1024, A.1026 Ligands: FLC.9, Q5B.20 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.1085, A:R.1085, A:W.1088, B:G.972, B:I.973, B:N.1024 Water bridges: A:D.1089 pi-Stacking: A:W.1088, A:W.1088, A:W.1088 COA.12: 17 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.1024, A.1026 Chain D: R.1085, H.1086, P.1087, W.1088 Ligands: Q5B.2 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.1085, D:R.1085, D:W.1088, C:G.972, C:I.973, C:N.1024 Water bridges: D:D.1089 pi-Stacking: D:W.1088, D:W.1088, D:W.1088 COA.17: 17 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.8 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:G.972, D:I.973, D:N.1024, C:R.1085, C:R.1085, C:W.1088 Water bridges: C:D.1089 pi-Stacking: C:W.1088, C:W.1088, C:W.1088

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

PO4.6: 8 residues within 4Å: Chain A: G.281, G.282, G.283, S.308, S.663, G.664, G.665 Ligands: Q5B.2 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 PO4.11: 8 residues within 4Å: Chain B: G.281, G.282, G.283, S.308, S.663, G.664, G.665 Ligands: Q5B.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.282, B:G.283, B:S.308, B:G.664, B:G.665 PO4.16: 8 residues within 4Å: Chain C: G.281, G.282, G.283, S.308, S.663, G.664, G.665 Ligands: Q5B.14 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.282, C:G.283, C:S.308, C:G.664, C:G.665 PO4.22: 8 residues within 4Å: Chain D: G.281, G.282, G.283, S.308, S.663, G.664, G.665 Ligands: Q5B.20 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.282, D:G.283, D:S.308, D:S.308, D:S.663, D:G.664, D:G.665

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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