SMTL ID : 8gr9.1

Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomyces cerevisiae in complex with oxaloacetate and coenzyme-A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 22 residues within 4Å: Chain A: R.66, L.292, H.293, A.296, L.328, V.333, I.334, P.335, G.336, Y.337, G.338, H.339, A.340, L.380, K.385, T.386, K.387, N.392, D.394 Chain B: K.184, I.438 Ligands: OAA.8 23 PLIP interactions: 17 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:L.292, A:I.334, A:I.334, A:G.336, A:Y.337, A:Y.337, A:K.387, A:N.392 Water bridges: A:H.339, A:R.343, A:R.343, A:K.387, A:K.387, A:N.388, B:K.184, B:K.184, B:K.184, B:S.437 Salt bridges: A:R.66, A:K.385, A:K.387, B:K.184 Hydrophobic interactions: B:I.438

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.37, E.74, R.87, T.118 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.87, A:R.87, A:T.118 Water bridges: A:E.74, B:E.447 GOL.3: 5 residues within 4Å: Chain A: P.152, D.154 Chain B: H.143, S.170, E.171 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.143, B:E.171 Water bridges: A:D.154 GOL.9: 6 residues within 4Å: Chain B: L.78, H.257, H.339, D.346, R.348, N.392 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.339, B:D.346, B:D.346, B:R.348 Water bridges: B:A.340, B:A.340

3 x K: POTASSIUM ION(Non-covalent)

K.4: 2 residues within 4Å: Chain A: E.299, E.302 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.302, H2O.8 K.5: 8 residues within 4Å: Chain A: G.260, N.261, V.262, H.265 Chain B: L.269, E.439, R.440, P.441 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.439, A:G.260, A:H.265 K.10: 8 residues within 4Å: Chain A: L.269, E.439, R.440, P.441 Chain B: G.260, N.261, V.262, H.265 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:G.260, B:H.265, A:E.439

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: R.440 Chain B: N.261, V.262, H.293 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: T.51, K.52 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: N.261, R.420 Ligand excluded by PLIP

1 x OAA: OXALOACETATE ION(Non-covalent)

OAA.8: 9 residues within 4Å: Chain A: H.257, N.261, H.293, H.339, R.348, F.416, R.420 Chain B: R.440 Ligands: COA.1 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.261 Hydrogen bonds: A:H.257, A:N.261, A:R.348, A:R.348 Water bridges: A:H.293, A:H.339, A:H.339 Salt bridges: A:H.257, A:H.257, A:H.293, A:H.339, A:R.348, A:R.420, B:R.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishio, K. et al., Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. Sci Adv (2023)

Release Date

2023-04-26

Peptides

Citrate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Citrate synthase

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