SMTL ID : 8g1f.1

Structure of ACLY-D1026A-products

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.40 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: V.56, K.58, K.64, R.65, R.66, K.68, V.74, P.109, F.110, V.111, H.113, N.203, P.204, L.215, D.216 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.58, A:R.65, A:R.66, A:P.109, A:V.111, A:H.113, A:D.216 Salt bridges: A:K.58, A:R.66, A:R.66, A:K.68 ADP.8: 15 residues within 4Å: Chain B: V.56, K.58, K.64, R.65, R.66, K.68, V.74, P.109, F.110, V.111, H.113, N.203, P.204, L.215, D.216 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.58, B:R.65, B:R.66, B:P.109, B:V.111, B:H.113, B:D.216, B:D.216 Salt bridges: B:K.58, B:R.66, B:R.66, B:K.68 ADP.14: 15 residues within 4Å: Chain C: V.56, K.58, K.64, R.65, R.66, K.68, V.74, P.109, F.110, V.111, H.113, N.203, P.204, L.215, D.216 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.58, C:R.65, C:R.66, C:P.109, C:V.111, C:H.113, C:D.216, C:D.216 Salt bridges: C:K.58, C:R.66, C:R.66, C:K.68 ADP.21: 15 residues within 4Å: Chain D: V.56, K.58, K.64, R.65, R.66, K.68, V.74, P.109, F.110, V.111, H.113, N.203, P.204, L.215, D.216 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.58, D:R.65, D:R.66, D:P.109, D:V.111, D:H.113, D:D.216 Salt bridges: D:K.58, D:R.66, D:R.66, D:K.68

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

UNL.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

Q5B.3: 31 residues within 4Å: Chain A: 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, A.624, T.625, V.626, G.665 Chain C: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: PO4.6, ACO.12 25 PLIP interactions: 19 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.572 Hydrogen bonds: A:G.309, A:S.343, A:S.343, A:N.346, A:N.346, A:F.347, A:T.348, A:T.348, A:R.379, A:S.574, A:S.577, A:S.577, A:E.599, A:E.599, 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: 30 residues within 4Å: Chain B: A.280, 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, E.599, A.624, T.625, V.626, G.665 Chain D: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: PO4.11, ACO.18 22 PLIP interactions: 6 interactions with chain D, 16 interactions with chain B Hydrogen bonds: D:I.970, D:I.970, 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:I.597 Salt bridges: D:K.964, D:K.1017, D:K.1018, D:K.1018, B:R.379, B:R.576 Hydrophobic interactions: B:F.347, B:F.572 Water bridges: B:S.574, B:S.574 Q5B.16: 31 residues within 4Å: Chain A: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain C: A.280, G.281, 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.664 Ligands: ACO.4, PO4.17 22 PLIP interactions: 6 interactions with chain A, 16 interactions with chain C Hydrogen bonds: A:I.970, A:I.970, C:G.309, 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:E.599 Salt bridges: A:K.964, A:K.1017, A:K.1018, A:K.1018, C:R.379, C:R.576 Hydrophobic interactions: C:F.572 Water bridges: C:S.574, C:S.574 Q5B.20: 32 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, G.281, 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.9, PO4.22 22 PLIP interactions: 6 interactions with chain B, 16 interactions with chain D Hydrogen bonds: B:I.970, B:I.970, D:G.309, 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:I.597 Salt bridges: B:K.964, B:K.1017, B:K.1018, B:K.1018, D:R.379, D:R.576 Hydrophobic interactions: D:F.347, D:E.599 Water bridges: D:S.574, D:S.574

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

ACO.4: 19 residues within 4Å: Chain A: A.903, A.938, I.970, M.971, G.972, I.973, G.974, H.975, R.976, V.977, N.1024, V.1025, A.1026 Chain B: R.1085, H.1086, P.1087, W.1088 Ligands: OAA.5, Q5B.16 13 PLIP interactions: 7 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:V.1025, A:A.1026, B:R.1085, B:R.1085, B:W.1088 pi-Stacking: B:W.1088, B:W.1088, B:W.1088 ACO.9: 18 residues within 4Å: Chain A: R.1085, H.1086, P.1087, W.1088 Chain B: A.903, A.938, I.970, M.971, G.972, I.973, G.974, H.975, R.976, N.1024, V.1025, A.1026 Ligands: OAA.10, Q5B.20 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.1026 Hydrogen bonds: B:G.972, B:I.973, B:I.973, B:R.976, B:V.1025, B:A.1026, A:R.1085, A:H.1086, A:W.1088 pi-Stacking: A:W.1088, A:W.1088, A:W.1088 ACO.12: 18 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.3, OAA.13 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:A.1026 Hydrogen bonds: C:G.972, C:I.973, C:I.973, C:R.976, C:V.1025, C:A.1026, D:R.1085, D:R.1085, D:W.1088 pi-Stacking: D:W.1088, D:W.1088, D:W.1088 ACO.18: 18 residues within 4Å: Chain C: R.1085, H.1086, P.1087, W.1088 Chain D: A.903, A.938, I.970, M.971, G.972, I.973, G.974, H.975, R.976, N.1024, V.1025, A.1026 Ligands: Q5B.7, OAA.19 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:A.1026 Hydrogen bonds: D:G.972, D:I.973, D:I.973, D:R.976, D:V.1025, D:A.1026, C:R.1085, C:H.1086, C:W.1088 pi-Stacking: C:W.1088, C:W.1088, C:W.1088

4 x OAA: OXALOACETATE ION(Non-covalent)

OAA.5: 7 residues within 4Å: Chain A: H.900, V.904, F.935, R.986, R.1065 Chain B: R.1085 Ligands: ACO.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.900, A:R.986, A:R.1065 Hydrogen bonds: B:R.1085 OAA.10: 7 residues within 4Å: Chain A: R.1085 Chain B: H.900, V.904, F.935, R.986, R.1065 Ligands: ACO.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.900, B:H.900, B:R.986, B:R.1065 Hydrogen bonds: A:R.1085 OAA.13: 7 residues within 4Å: Chain C: H.900, V.904, F.935, R.986, R.1065 Chain D: R.1085 Ligands: ACO.12 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.1085 Salt bridges: C:H.900, C:H.900, C:R.986, C:R.1065 OAA.19: 7 residues within 4Å: Chain C: R.1085 Chain D: H.900, V.904, F.935, R.986, R.1065 Ligands: ACO.18 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.900, C:R.1085 Salt bridges: D:H.900, D:H.900, D:R.986, D:R.1065

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

PO4.6: 9 residues within 4Å: Chain A: G.281, G.282, G.283, S.308, S.663, G.664, G.665, H.760 Ligands: Q5B.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.282, A:G.283, A:S.308, A:G.664, A:G.665 Salt bridges: A:H.760 PO4.11: 9 residues within 4Å: Chain B: G.281, G.282, G.283, S.308, S.663, G.664, G.665, H.760 Ligands: Q5B.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.282, B:G.283, B:S.308, B:S.663, B:S.663, B:G.664, B:G.665 Salt bridges: B:H.760 PO4.17: 9 residues within 4Å: Chain C: G.281, G.282, G.283, S.308, S.663, G.664, G.665, H.760 Ligands: Q5B.16 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.282, C:G.283, C:S.308, C:S.308, C:S.663, C:S.663, C:G.664, C:G.665 Salt bridges: C:H.760 PO4.22: 9 residues within 4Å: Chain D: G.281, G.282, G.283, S.308, S.663, G.664, G.665, H.760 Ligands: Q5B.20 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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