SMTL ID : 7rmp.1

Structure of ACLY D1026A - substrates-asym

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: V.56, K.58, I.63, R.65, R.66, G.67, V.72, F.110, V.111, H.113, E.118, G.139, V.140, N.203, P.204, L.215, D.216 10 PLIP interactions: 10 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:N.203, A:D.216 Salt bridges: A:R.65 ADP.7: 15 residues within 4Å: Chain B: V.56, K.58, R.65, R.66, V.72, E.108, P.109, F.110, V.111, H.113, E.118, N.203, P.204, L.215, D.216 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.58, B:R.65, B:R.66, B:R.66, B:E.108, B:V.111, B:H.113, B:N.203, B:D.216 ADP.16: 14 residues within 4Å: Chain D: V.56, K.58, R.65, R.66, G.67, V.74, F.110, H.113, G.139, V.140, N.203, P.204, L.215, D.216 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.58, D:R.65, D:R.66, D:G.67, D:V.140, 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: 28 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, S.574, R.576, S.577, I.597, V.626, N.638, G.665 Chain C: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: PO4.6, COA.12 21 PLIP interactions: 6 interactions with chain C, 15 interactions with chain A Hydrogen bonds: C:I.970, C:I.970, 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.574, A:S.574 Salt bridges: C:K.964, C:K.1017, C:K.1018, C:K.1018, A:R.379, A:R.576 Hydrophobic interactions: A:I.597 Water bridges: A:I.597, A:T.625 Q5B.8: 30 residues within 4Å: Chain B: A.280, G.281, Y.307, S.308, G.309, A.345, N.346, F.347, T.348, R.379, Q.505, F.533, F.572, S.574, R.576, S.577, I.597, E.599, V.626, N.638, G.664 Chain D: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: PO4.11, COA.15 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:F.347 Hydrogen bonds: B:G.309, B:A.310, B:N.346, B:N.346, B:F.347, B:T.348, B:T.348, B:S.574, B:S.574, B:S.577, B:S.577, B:N.638, B:G.664, D:I.970, D:I.970 Salt bridges: B:R.379, B:R.576, D:K.964, D:K.1017, D:K.1018, D:K.1018 Q5B.17: 28 residues within 4Å: Chain B: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain D: A.280, G.281, S.308, G.309, A.345, N.346, F.347, T.348, R.379, Q.505, F.533, F.572, S.574, R.576, S.577, I.597, A.598, V.626, N.638 Ligands: COA.10, PO4.19 18 PLIP interactions: 6 interactions with chain B, 12 interactions with chain D Hydrogen bonds: B:I.970, B:I.970, D:A.280, D:G.309, D:N.346, D:N.346, D:F.347, D:T.348, D:T.348, D:S.574, D:R.576, D:N.638 Salt bridges: B:K.964, B:K.1017, B:K.1018, B:K.1018, D:R.379, D:R.576

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, R.1065 Chain B: R.1085 Ligands: COA.5 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.900 Hydrogen bonds: A:G.936 Salt bridges: A:H.900, A:H.900, A:R.986, A:R.1065, B:R.1085 FLC.9: 8 residues within 4Å: Chain B: H.900, V.904, F.935, G.936, A.938, R.986, R.1065 Ligands: COA.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.900 Hydrogen bonds: B:G.936, B:R.1065 Salt bridges: B:H.900, B:H.900, B:R.986, B:R.1065 FLC.13: 8 residues within 4Å: Chain C: H.900, V.904, F.935, G.936, A.938, F.1061, R.1065 Ligands: COA.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.936, C:R.1065 Salt bridges: C:H.900, C:H.900, C:R.1065 FLC.18: 9 residues within 4Å: Chain C: R.1085 Chain D: H.900, V.904, F.935, G.936, R.986, V.1025, R.1065 Ligands: COA.15 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Salt bridges: C:R.1085, D:H.900, D:H.900, D:R.986 Hydrophobic interactions: D:H.900 Hydrogen bonds: D:G.936, D:R.1065, D:R.1065

2 x UNL: UNKNOWN LIGAND

UNL.4: 1 residues within 4Å: Chain B: M.823 No protein-ligand interaction detected (PLIP) UNL.14: 2 residues within 4Å: Chain C: L.833 Chain D: L.833 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.833

4 x COA: COENZYME A(Non-covalent)

COA.5: 14 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 Ligands: FLC.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.970, A:I.970, A:G.972, A:I.973, A:I.973, A:N.1020 Salt bridges: A:K.1018, A:K.1018 COA.10: 16 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 Ligands: FLC.9, Q5B.17 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.1085, A:R.1085, A:W.1088, B:G.972, B:I.973, B:R.976, B:N.1024 pi-Stacking: A:W.1088, A:W.1088, A:W.1088 COA.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.1020, N.1024, A.1026 Chain D: R.1085, H.1086, P.1087, W.1088 Ligands: Q5B.2, FLC.13 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:G.972, C:I.973, C:N.1020, C:N.1024, D:R.1085, D:H.1086, D:W.1088 pi-Stacking: D:W.1088, D:W.1088, D:W.1088 COA.15: 17 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, A.1026 Ligands: Q5B.8, FLC.18 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:R.976, D:N.1024, C:R.1085, C:R.1085, C:W.1088 pi-Stacking: C:W.1088, C:W.1088, C:W.1088

3 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:G.664, A:G.665, A:M.666 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 PO4.19: 8 residues within 4Å: Chain D: G.281, G.282, G.283, S.308, S.663, G.664, G.665 Ligands: Q5B.17 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.282, D:G.283, D:S.308, 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

Related Entries With Identical Sequence