SMTL ID : 6uuw.1

Structure of human ATP citrate lyase E599Q mutant in complex with Mg2+, citrate, ATP and CoA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: V.56, K.58, R.65, R.66, G.67, P.109, F.110, V.111, H.113, N.203, P.204, L.215, D.216 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.58, A:R.65, A:R.66, A:R.66, A:G.67, A:P.109, A:V.111, A:D.216 Salt bridges: A:K.58 ADP.5: 13 residues within 4Å: Chain B: V.56, K.58, R.65, R.66, E.108, P.109, F.110, V.111, H.113, 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:E.108, B:V.111, B:H.113, B:N.203, B:N.203, B:D.216 Salt bridges: B:K.58 ADP.8: 14 residues within 4Å: Chain C: V.56, K.58, K.64, R.65, R.66, E.108, P.109, F.110, V.111, H.113, N.203, P.204, L.215, D.216 13 PLIP interactions: 13 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:N.203, C:D.216, C:D.216 Salt bridges: C:K.58, C:R.66 ADP.12: 13 residues within 4Å: Chain D: V.56, K.58, R.65, R.66, G.67, P.109, F.110, V.111, H.113, 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:R.66, D:G.67, D:P.109, D:V.111, D:D.216 Salt bridges: D:K.58

4 x COA: COENZYME A(Non-covalent)

COA.2: 23 residues within 4Å: Chain A: G.309, F.347, Q.505, F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, Q.599, A.624, T.625, V.626 Chain C: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: Y2A.3 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.347, A:I.597 Hydrogen bonds: A:S.574, A:S.577, A:Q.599, A:T.625, C:I.970, C:I.970 Salt bridges: A:R.576, C:K.964, C:K.1017, C:K.1018, C:K.1018 COA.6: 22 residues within 4Å: Chain B: G.261, G.309, F.347, Q.505, F.533, F.572, A.573, S.574, R.576, S.577, I.597, Q.599, T.625, V.626 Chain D: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Ligands: Y2A.7 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:F.347, B:I.597 Hydrogen bonds: B:S.574, B:S.577, B:I.597, B:Q.599, D:I.970, D:I.970 Salt bridges: B:R.576, D:K.964, D:K.1017, D:K.1018, D:K.1018 COA.9: 23 residues within 4Å: Chain A: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain C: G.309, F.347, Q.505, F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, Q.599, A.624, T.625, V.626 Ligands: Y2A.10 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:F.347, C:I.597 Hydrogen bonds: C:S.574, C:S.577, C:Q.599, C:T.625, A:I.970, A:I.970 Salt bridges: C:R.576, A:K.964, A:K.1017, A:K.1018, A:K.1018 COA.13: 23 residues within 4Å: Chain B: K.964, L.969, I.970, I.973, K.1017, K.1018, L.1021 Chain D: G.309, F.347, Q.505, F.533, F.572, A.573, S.574, R.576, S.577, I.597, A.598, Q.599, A.624, T.625, V.626 Ligands: Y2A.14 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:F.347, D:I.597 Hydrogen bonds: D:S.574, D:S.577, D:Q.599, D:T.625, B:I.970, B:I.970 Salt bridges: D:R.576, B:K.964, B:K.1017, B:K.1018, B:K.1018

4 x Y2A: (2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy)ethyl]butanedioic acid(Non-covalent)

Y2A.3: 17 residues within 4Å: Chain A: A.280, G.281, G.282, G.283, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, S.663, G.664, G.665, H.760 Ligands: COA.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.282, A:G.283, A:G.309, A:N.346, A:N.346, A:F.347, A:T.348, A:T.348, A:T.348, A:T.348, A:G.664, A:G.665 Water bridges: A:A.284 Salt bridges: A:R.379, A:H.760 Y2A.7: 16 residues within 4Å: Chain B: A.280, G.281, G.282, G.283, S.308, G.309, A.345, N.346, F.347, T.348, R.379, S.663, G.664, G.665, H.760 Ligands: COA.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.347 Hydrogen bonds: B:G.282, B:G.283, B:G.309, B:A.310, B:S.343, B:N.346, B:N.346, B:F.347, B:T.348, B:T.348, B:G.664, B:G.665 Water bridges: B:A.284, B:Q.599, B:H.760 Salt bridges: B:R.379, B:H.760 Y2A.10: 17 residues within 4Å: Chain C: A.280, G.281, G.282, G.283, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, S.663, G.664, G.665, H.760 Ligands: COA.9 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.282, C:G.283, C:G.309, C:S.343, C:N.346, C:N.346, C:F.347, C:T.348, C:T.348, C:G.664, C:G.665 Water bridges: C:A.284, C:Q.599, C:H.760 Salt bridges: C:R.379, C:H.760 Y2A.14: 17 residues within 4Å: Chain D: A.280, G.281, G.282, G.283, S.308, G.309, S.343, A.345, N.346, F.347, T.348, R.379, S.663, G.664, G.665, H.760 Ligands: COA.13 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.282, D:G.283, D:G.309, D:N.346, D:N.346, D:F.347, D:T.348, D:T.348, D:T.348, D:T.348, D:G.664, D:G.665 Water bridges: D:A.284 Salt bridges: D:R.379, D:H.760

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

UNL.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNL.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, X. et al., Molecular basis for acetyl-CoA production by ATP-citrate lyase. Nat.Struct.Mol.Biol. (2020)

Release Date

2019-12-25

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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