SMTL ID : 7msr.1

Human E105Qa GTP-specific succinyl-CoA synthetase complexed with succinyl-phosphate, magnesium ion and desulfo-coenzyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DCA: DESULFO-COENZYME A(Non-covalent)

DCA.1: 30 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 Chain B: G.298, I.329 Ligands: MG.5, ZNS.7 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.27, A:I.145, B:I.329 Hydrogen bonds: A:G.22, A:T.24, A:K.26, A:Q.27, A:I.103, A:Q.105, B:G.298 Water bridges: A:Q.21, A:G.25, A:G.28, A:A.87, B:G.298 Salt bridges: A:K.50

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

EDO.2: 6 residues within 4Å: Chain A: V.285, S.286, M.287, S.288, Q.291, T.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.285, A:M.287, A:S.288

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: Y.3, K.116, L.120, R.126, N.192, G.193, T.194, D.195, D.198 Chain B: N.126 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.116, A:N.192, A:D.198, B:N.126 Water bridges: A:R.126, A:N.192 GOL.4: 4 residues within 4Å: Chain A: T.54, H.55, L.56, G.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.54, A:H.55, A:L.56, A:G.57 GOL.6: 11 residues within 4Å: Chain A: R.161, I.186, D.189, P.190, N.192, D.195, F.196, G.220, N.221, A.222 Chain B: R.123 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.161, A:P.190, A:N.192, B:R.123, B:R.123 Water bridges: A:R.161, A:N.221, A:A.222 GOL.8: 9 residues within 4Å: Chain B: V.354, R.355, L.356, Q.365, L.368, N.369, I.375, S.377, A.378 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.354, B:L.356, B:Q.365, B:N.369 Water bridges: B:L.368, B:N.369

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: Q.105 Chain B: G.272, A.273 Ligands: DCA.1, ZNS.7 No protein-ligand interaction detected (PLIP)

1 x ZNS: 4-oxo-4-(phosphonooxy)butanoic acid(Non-covalent)

ZNS.7: 21 residues within 4Å: Chain A: P.133, I.145, R.161, S.162, G.163, T.164, Y.167, H.259 Chain B: N.271, G.272, A.273, G.274, L.275, G.298, F.326, G.327, G.328, I.329, V.330 Ligands: DCA.1, MG.5 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:N.271, B:A.273, B:G.274, B:G.328, B:I.329, B:V.330, A:S.162, A:G.163, A:T.164, A:T.164, A:Y.167 Water bridges: B:G.272, B:G.272 Hydrophobic interactions: A:T.164 Salt bridges: A:H.259

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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