SMTL ID : 8zvt.1

Human citrate synthase intermediate 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x OAA: OXALOACETATE ION(Non-covalent)

OAA.1: 9 residues within 4Å: Chain A: H.238, N.242, H.274, H.320, R.329, F.397, R.401 Chain B: R.421 Ligands: ACY.2 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Salt bridges: B:R.421, A:H.238, A:H.238, A:H.274, A:H.320, A:R.329, A:R.401 Hydrophobic interactions: A:N.242 Hydrogen bonds: A:N.242, A:R.329, A:R.329 Water bridges: A:H.274 OAA.4: 9 residues within 4Å: Chain A: R.421 Chain B: H.238, N.242, H.274, H.320, R.329, F.397, R.401 Ligands: ACY.5 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B Salt bridges: A:R.421, B:H.238, B:H.238, B:H.274, B:H.320, B:R.329, B:R.401 Hydrophobic interactions: B:N.242 Hydrogen bonds: B:N.242, B:R.329, B:R.329 Water bridges: B:H.274

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 7 residues within 4Å: Chain A: H.274, H.320, R.329, D.375, F.397 Ligands: OAA.1, COA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.320 Salt bridges: A:R.329 ACY.5: 7 residues within 4Å: Chain B: H.274, H.320, R.329, D.375, F.397 Ligands: OAA.4, COA.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.320 Salt bridges: B:R.329

2 x COA: COENZYME A(Non-covalent)

COA.3: 19 residues within 4Å: Chain A: R.46, A.277, L.309, V.314, V.315, P.316, G.317, Y.318, G.319, H.320, A.321, L.361, Q.364, K.366, A.367, K.368, N.373, D.375 Ligands: ACY.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:V.315, A:G.317, A:Y.318, A:Y.318, A:Y.318, A:Q.364, A:N.373 Salt bridges: A:R.46, A:R.46, A:K.368 COA.6: 19 residues within 4Å: Chain B: R.46, A.277, L.309, V.314, V.315, P.316, G.317, Y.318, G.319, H.320, A.321, L.361, Q.364, K.366, A.367, K.368, N.373, D.375 Ligands: ACY.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:V.315, B:G.317, B:Y.318, B:Y.318, B:Y.318, B:Q.364, B:N.373 Salt bridges: B:R.46, B:R.46, B:K.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L.Y. et al., Human citrate synthase intermediate 3. To Be Published

Release Date

2025-06-18

Peptides

Citrate synthase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Citrate synthase, mitochondrial