SMTL ID : 8z03.1

Lactate bound to human GTP-specific succinyl-CoA synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-mer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 23 residues within 4Å: Chain A: G.22, T.24, G.25, K.26, Q.27, T.46, T.47, P.48, K.50, Y.79, V.80, P.81, P.82, F.84, I.103, T.104, E.105, N.131, C.132, P.133, I.145 Chain B: G.298 Ligands: PO4.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.27, A:T.104 Hydrogen bonds: A:G.22, A:T.24, A:K.26, A:Q.27, A:I.103, A:E.105, B:G.298 Water bridges: A:G.28, A:E.91 Salt bridges: A:K.50

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

PO4.2: 10 residues within 4Å: Chain A: S.162, G.163, T.164, H.259 Chain B: G.272, A.273, G.274 Ligands: COA.1, 2OP.3, MG.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.163, A:T.164, B:A.273, B:G.274 Salt bridges: A:H.259

1 x 2OP: (2S)-2-HYDROXYPROPANOIC ACID(Non-covalent)

2OP.3: 13 residues within 4Å: Chain A: I.145, T.164, Y.167 Chain B: N.271, G.272, L.296, F.326, G.327, G.328, I.329, V.330 Ligands: PO4.2, MG.4 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.329, A:I.145, A:Y.167 Hydrogen bonds: B:N.271, B:G.328, B:I.329, B:V.330

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: G.272, G.298 Ligands: PO4.2, 2OP.3 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: 2OP.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, R. et al., Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and gliomagenesis. Cell Metab. (2024)

Release Date

2024-12-11

Peptides

Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial: A
Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial

Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial

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