SMTL ID : 6no5.2 (1 other biounit)

ADP bound to K46bE&K114bD mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: Q.20, V.48, K.50, G.56, G.57, R.58, G.59, V.71, C.110, G.111, A.112, V.113, I.115, E.118, G.141, N.210, P.211, L.227, D.228 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.20, A:K.50, A:G.57, A:R.58, A:G.59, A:G.111, A:V.113, A:E.118, A:N.210, A:D.228 Water bridges: A:R.58, A:R.58, A:N.210, A:D.228 Salt bridges: A:K.50, A:R.58, A:R.58 ADP.4: 19 residues within 4Å: Chain B: Q.20, V.48, K.50, G.56, G.57, R.58, G.59, V.71, C.110, G.111, A.112, V.113, I.115, E.118, N.210, P.211, L.227, D.228 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.20, B:K.50, B:G.57, B:R.58, B:G.59, B:G.111, B:V.113, B:E.118, B:N.210, B:D.228 Water bridges: B:R.58, B:R.58, B:N.210, B:D.228 Salt bridges: B:K.50, B:R.58, B:R.58

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.210, P.211, D.228 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.210, A:D.228, H2O.1, H2O.3 MG.5: 4 residues within 4Å: Chain B: N.210, P.211, D.228 Ligands: ADP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.210, B:D.228, H2O.4, H2O.6

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 9 residues within 4Å: Chain A: D.114, E.216, T.217, P.218, D.220 Chain B: P.218, T.219, D.220 Ligands: NH4.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.220, B:D.220 NH4.6: 8 residues within 4Å: Chain A: P.218, T.219, D.220 Chain B: D.114, E.216, T.217, D.220 Ligands: NH4.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.114, B:E.216, B:D.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., ATP-specificity of succinyl-CoA synthetase from Blastocystis hominis. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-07-17

Peptides

Succinate--CoA ligase [ADP-forming] subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Succinate--CoA ligase [ADP-forming] subunit beta

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