SMTL ID : 5tdz.1

TEV Cleaved Human ATP Citrate Lyase Bound to Tartrate and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-oligomer

Ligands

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 13 residues within 4Å: Chain A: A.280, G.281, S.308, G.309, A.310, S.343, A.345, N.346, F.347, T.348, R.379 Chain B: G.179 Ligands: PO4.4 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.309, A:A.310, A:S.343, A:N.346, A:N.346, A:F.347, A:T.348, A:T.348, B:G.179 Water bridges: A:A.280, A:R.379 Salt bridges: A:R.379

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

ADP.2: 20 residues within 4Å: Chain A: V.56, K.58, K.64, R.65, R.66, G.67, K.68, V.72, V.74, E.108, P.109, F.110, V.111, H.113, E.118, N.203, P.204, L.215, D.216 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.65, A:R.66, A:G.67, A:P.109, A:V.111, A:E.118, A:N.203 Water bridges: A:K.58, A:R.65, A:R.65, A:R.65, A:R.65 Salt bridges: A:K.58, A:R.65, A:R.66, A:R.66

1 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.3, H2O.5

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

PO4.4: 10 residues within 4Å: Chain A: G.281, G.282, G.283, S.308 Chain B: S.177, G.178, G.179, M.180, H.274 Ligands: TLA.1 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.282, A:G.283, B:S.177, B:G.178, B:G.179 Water bridges: A:A.280, A:G.309, A:S.343, A:S.343, A:S.343

1 x ADN: ADENOSINE(Non-covalent)

ADN.5: 8 residues within 4Å: Chain A: R.33, D.37, T.38, D.39, R.42, L.43, D.46 Ligands: GOL.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.33, A:D.39, A:D.39, A:R.42, A:R.42 pi-Cation interactions: A:R.42

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.33, V.34, T.35, D.37, T.38, L.43 Ligands: ADN.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.33, A:R.33, A:T.35, A:T.38 GOL.9: 9 residues within 4Å: Chain A: H.410, M.411, T.412 Chain B: I.187, F.304, D.305, E.306, L.307, G.308 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.305, B:L.307, B:G.308 Water bridges: B:D.305, B:D.305, A:M.411

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 6 residues within 4Å: Chain A: Y.124, T.126, Y.131, L.133, A.149, K.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.124, A:K.151 PGE.10: 8 residues within 4Å: Chain A: V.156, D.157, E.193, Y.196 Chain B: Y.93, A.118, L.119, K.122 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.158, A:E.193 Hydrogen bonds: B:K.122

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 9 residues within 4Å: Chain B: R.9, C.33, S.34, P.145, G.146, C.147, Y.166, R.167, P.168 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.33, B:G.146 Water bridges: B:R.9

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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