SMTL ID : 5tdf.1

TEV Cleaved Human ATP Citrate Lyase Bound to 4S hydroxycitrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 7A3: 3-C-carboxy-2-deoxy-D-erythro-pentaric acid(Non-covalent)

7A3.1: 17 residues within 4Å: Chain A: A.280, G.281, G.282, S.308, G.309, A.310, S.343, A.345, N.346, F.347, T.348, R.379 Chain B: V.140, G.178, G.179, H.274 Ligands: MG.8 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.309, A:N.346, A:N.346, A:F.347, A:T.348, A:T.348, A:T.348, A:T.348 Salt bridges: A:R.379 Water bridges: B:G.178

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

ADP.2: 20 residues within 4Å: Chain A: V.56, K.58, R.65, R.66, G.67, K.68, V.72, V.74, E.108, P.109, F.110, V.111, H.113, E.118, G.139, N.203, P.204, L.215, D.216 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.65, A:R.66, A:G.67, A:P.109, A:V.111, A:G.139 Water bridges: A:K.58, A:E.118, A:E.118, A:N.203 Salt bridges: A:K.58, A:R.66, A:R.66

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.203, P.204, D.216 Ligands: ADP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.203, A:D.216, H2O.10, H2O.13 MG.8: 4 residues within 4Å: Chain A: S.263, G.282 Chain B: H.274 Ligands: 7A3.1 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: Y.124, T.126, Y.131, K.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.124, A:K.151 GOL.5: 8 residues within 4Å: Chain A: R.33, V.34, T.35, D.37, T.38, D.39, L.43 Ligands: ADE.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.33, A:T.35, A:T.38 Water bridges: A:R.33 GOL.6: 5 residues within 4Å: Chain A: L.152, E.158, D.164, K.167, H.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.164, A:K.167, A:H.168 GOL.9: 8 residues within 4Å: Chain A: H.410, M.411 Chain B: I.187, F.304, D.305, E.306, L.307, G.308 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.304, B:L.307, B:G.308 Water bridges: B:D.305, B:D.305, B:D.305, B:E.309 GOL.10: 5 residues within 4Å: Chain B: F.299, I.310, S.313, V.314, D.317 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.313 GOL.11: 7 residues within 4Å: Chain B: W.257, N.290, Q.291, K.294, V.300, P.301, R.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.294 Water bridges: B:Q.291, B:Q.291, B:R.302

1 x ADE: ADENINE(Non-covalent)

ADE.7: 7 residues within 4Å: Chain A: D.37, T.38, D.39, R.42, L.43, D.46 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.39, A:D.39 Water bridges: A:D.46 pi-Cation interactions: A:R.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, J. et al., Binding of hydroxycitrate to human ATP-citrate lyase. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-08-09

Peptides

ATP-citrate synthase: A
ATP-citrate synthase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-citrate synthase

ATP-citrate synthase

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