SMTL ID : 7mst.1

Phosphorylated human E105Qa GTP-specific succinyl-CoA synthetase complexed with coenzyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

hetero-1-1-mer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 27 residues within 4Å: Chain A: Q.21, G.22, T.24, G.25, K.26, Q.27, G.28, T.46, T.47, P.48, K.50, Y.79, V.80, P.81, P.82, F.84, A.87, A.88, I.103, T.104, Q.105, N.131, C.132, P.133, I.145, G.163, H.259 18 PLIP interactions: 18 interactions with chain A 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:Q.105 Water bridges: A:Q.21, A:G.25, A:G.25, A:G.25, A:G.28, A:K.50, A:E.91 Salt bridges: A:K.26, A:K.26, A:K.50

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: R.161, I.186, D.189, P.190, F.191, N.192, D.195, G.220, A.222 Chain B: R.123 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.190, A:N.192, B:R.123, B:R.123 Water bridges: A:R.161, A:G.187, A:N.221 GOL.3: 11 residues within 4Å: Chain A: Y.3, K.116, L.119, L.120, R.126, N.192, G.193, T.194, D.195, D.198 Chain B: N.126 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.116, A:N.192 Water bridges: A:R.7, A:R.7, A:R.126, A:N.192, A:D.198 GOL.5: 4 residues within 4Å: Chain A: G.51, G.52, N.62, E.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.66 Water bridges: A:G.52

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: T.4, R.7, I.197, E.201, F.229, H.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.7, A:R.7, A:E.201 EDO.6: 10 residues within 4Å: Chain A: I.218, G.248, L.249, T.250, A.251, I.264, G.270, A.271, K.272, E.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.248, A:A.271, A:K.272, A:E.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase. Acta Crystallogr.,Sect.F (2022)

Release Date

2022-10-12

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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