SMTL ID : 5cae.1

Succinate bound to pig GTP-specific succinyl-CoA synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 25 residues within 4Å: Chain A: G.21, T.23, G.24, K.25, Q.26, T.45, T.46, P.47, K.49, Y.78, V.79, P.80, P.81, F.83, A.87, I.102, T.103, E.104, N.130, C.131, P.132, I.144 Chain B: G.298 Ligands: PO4.4, SIN.6 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.26 Hydrogen bonds: A:G.21, A:T.23, A:T.23, A:K.25, A:Q.26, A:I.102, A:E.104, B:G.298 Water bridges: A:Q.20, A:G.27, A:T.45, B:G.299 Salt bridges: A:K.49

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: R.6, F.228 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.160, I.185, P.189, N.191, A.221 Chain B: R.123 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.160, A:P.189, A:N.191, B:R.123 Water bridges: A:R.160 GOL.7: 3 residues within 4Å: Chain B: A.28, G.77, Q.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.77 Water bridges: B:Q.78

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

PO4.4: 10 residues within 4Å: Chain A: S.161, G.162, T.163, H.258 Chain B: G.272, A.273, G.274 Ligands: COA.1, MG.5, SIN.6 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.273, B:G.274, B:L.275, A:S.161, A:G.162, A:T.163 Salt bridges: A:H.258

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: H.258 Ligands: PO4.4, SIN.6 No protein-ligand interaction detected (PLIP)

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.6: 14 residues within 4Å: Chain A: I.144, T.163, Y.166 Chain B: N.271, G.297, G.298, F.326, G.327, G.328, I.329, V.330 Ligands: COA.1, PO4.4, MG.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.329, B:V.330, A:T.163 Hydrogen bonds: B:N.271, B:G.298, B:G.328, B:I.329, B:V.330 Water bridges: B:A.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., Structural basis for the binding of succinate to succinyl-CoA synthetase. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-06-29

Peptides

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

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

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