SMTL ID : 8gqz.1

Crystal structure of mitochondrial citrate synthase (Cit1) from Saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: D.173 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.189, A:D.173 Hydrogen bonds: A:D.173

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

CL.2: 5 residues within 4Å: Chain A: I.457, R.459 Chain B: N.280, V.281, H.312 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: H.276, N.280, H.312, R.439 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: N.280, V.281, H.312 Chain B: I.457, R.459 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: H.276, N.280, H.312, R.439 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 5 residues within 4Å: Chain A: K.56, I.60, E.93, R.106, I.449 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.56, A:I.60, A:I.449 Water bridges: A:K.56, B:T.465 Salt bridges: A:K.56, A:R.106 ACT.8: 5 residues within 4Å: Chain B: K.56, I.60, E.93, R.106, I.449 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Water bridges: A:T.465, B:K.56 Hydrophobic interactions: B:I.60, B:I.449 Hydrogen bonds: B:E.93 Salt bridges: B:K.56, B:R.106

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain B: P.380, D.381 No protein-ligand interaction detected (PLIP)

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