SMTL ID : 6xru.1

GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme A, magnesium ions and succinates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

DCA.1: 31 residues within 4Å: Chain A: Q.20, G.21, T.23, G.24, K.25, Q.26, G.27, T.45, T.46, P.47, K.49, Y.78, V.79, P.80, P.81, F.83, A.86, A.87, I.102, T.103, E.104, N.130, C.131, P.132, I.144, G.162 Chain B: G.298, G.299, I.329 Ligands: SIN.7, MG.11 19 PLIP interactions: 1 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:G.298, A:G.21, A:T.23, A:T.23, A:K.25, A:Q.26, A:I.102, A:E.104 Hydrophobic interactions: A:Q.26, A:T.103, A:I.144 Water bridges: A:Q.20, A:G.24, A:G.24, A:K.49, A:K.49, A:K.49, A:E.90 Salt bridges: A:K.49

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 9 residues within 4Å: Chain A: G.253, R.255, I.262, A.264, G.265 Chain B: T.201, Q.202, K.222, N.224 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.201, B:T.201, A:G.265 Water bridges: B:Q.202, B:K.222, B:K.222, A:R.255 Salt bridges: B:K.222, A:R.255 Hydrophobic interactions: A:I.262 SIN.7: 16 residues within 4Å: Chain A: P.132, I.144, G.162, T.163, Y.166 Chain B: N.271, G.272, G.298, F.326, G.327, G.328, I.329, V.330 Ligands: DCA.1, PO4.6, MG.11 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.329, A:T.163 Hydrogen bonds: B:N.271, B:G.328, B:I.329, B:V.330, A:G.162, A:Y.166 Water bridges: B:A.273, B:G.298

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Y.37, P.137, G.138, H.150, K.151, K.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.150, A:K.152 Water bridges: A:G.138 GOL.4: 4 residues within 4Å: Chain A: L.248, T.249, K.271 Chain B: F.284 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.248 GOL.8: 9 residues within 4Å: Chain A: K.267 Chain B: L.120, D.122, R.123, S.124, V.129, V.131, K.153, Q.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.122, B:R.123, B:K.153 GOL.9: 6 residues within 4Å: Chain B: A.28, N.29, L.32, G.77, Q.78, K.81 No protein-ligand interaction detected (PLIP)

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

EDO.5: 6 residues within 4Å: Chain A: V.284, S.285, M.286, S.287, Q.290, T.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.285, A:M.286, A:S.287 EDO.10: 5 residues within 4Å: Chain B: F.231, R.232, Q.233, K.234, D.235 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.231, B:K.234, B:D.235, B:D.235 Water bridges: B:I.236

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

PO4.6: 10 residues within 4Å: Chain A: S.161, G.162, T.163, H.258 Chain B: G.272, A.273, G.274, L.275 Ligands: SIN.7, MG.11 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.161, A:G.162, A:T.163, A:T.163, A:T.163, B:A.273, B:G.274 Salt bridges: A:H.258

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.11: 7 residues within 4Å: Chain B: G.272, A.273, G.297, G.298 Ligands: DCA.1, PO4.6, SIN.7 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: K.222 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase. Acta Crystallogr.,Sect.D (2021)

Release Date

2021-03-10

Peptides

Succinyl-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

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

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

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