SMTL ID : 4xx0.1

CoA bound to pig GTP-specific succinyl-CoA synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 21 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.26, A:T.103 Hydrogen bonds: A:G.21, A:T.23, A:T.23, A:K.25, A:Q.26, A:F.83, A:I.102, A:E.104 Water bridges: A:Q.20, A:Q.20, A:G.27 Salt bridges: A:K.49

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

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

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: Q.121, G.122, K.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.122, A:K.123 Water bridges: A:Q.121 Salt bridges: A:K.123 SO4.4: 6 residues within 4Å: Chain A: G.253, R.254, R.255 Chain B: D.227, K.258 Ligands: SO4.8 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.255, B:D.227 Salt bridges: A:R.254, A:R.255, B:K.258 SO4.5: 3 residues within 4Å: Chain A: T.53, H.54, L.55 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.53, A:L.55 Water bridges: A:T.53, A:G.56 Salt bridges: A:H.54 SO4.7: 3 residues within 4Å: Chain B: T.70, K.71, D.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.70, B:K.71, B:D.72 SO4.8: 5 residues within 4Å: Chain A: R.255 Chain B: M.1, N.224, F.225 Ligands: SO4.4 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.225 Water bridges: B:T.201, B:F.225 Salt bridges: A:R.255 SO4.9: 3 residues within 4Å: Chain B: G.52, G.53, R.54 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.53, B:R.54 Water bridges: B:G.55 Salt bridges: B:R.54

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: K.115, L.119, N.191, G.192, T.193, D.194, D.197 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.115, A:N.191, A:D.197 Water bridges: A:R.6, A:R.6, A:N.191 GOL.10: 4 residues within 4Å: Chain B: A.28, G.77, Q.78, K.81 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.81 GOL.11: 3 residues within 4Å: Chain B: K.163, D.164, S.165 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.164, B:S.165, B:S.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., Structure of GTP-specific succinyl-CoA synthetase in complex with CoA. Acta Crystallogr.,Sect.F (2015)

Release Date

2015-08-12

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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