- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.28 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 4 residues within 4Å:- Chain A: D.305, N.338, V.340
- Ligands: TPP.4
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.305, A:V.340, H2O.1
MG.9: 4 residues within 4Å:- Chain B: D.305, N.338, V.340
- Ligands: TPP.10
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.305, B:V.340, H2O.13
- 2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
TPP.4: 21 residues within 4Å:- Chain A: H.208, R.209, S.269, H.270, L.271, G.304, D.305, S.306, A.307, Q.311, N.338, V.340, G.341, H.408
- Chain B: Q.564, L.607, E.609, Q.633, F.637
- Ligands: MG.3, DW3.7
16 PLIP interactions:1 interactions with chain B, 15 interactions with chain A- pi-Stacking: B:F.637
- Hydrogen bonds: A:S.269, A:L.271, A:D.305, A:S.306, A:A.307, A:N.338, A:V.340
- Water bridges: A:H.208, A:G.304, A:G.304, A:F.342, A:H.408
- Salt bridges: A:H.208, A:R.209, A:H.408
TPP.10: 21 residues within 4Å:- Chain A: Q.564, L.607, E.609, Q.633, F.637
- Chain B: H.208, R.209, S.269, H.270, L.271, G.304, D.305, S.306, A.307, Q.311, N.338, V.340, G.341, H.408
- Ligands: DW3.6, MG.9
18 PLIP interactions:15 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:S.269, B:L.271, B:D.305, B:S.306, B:A.307, B:N.338, B:V.340
- Water bridges: B:H.208, B:R.209, B:G.304, B:F.342, B:F.342
- Salt bridges: B:H.208, B:R.209, B:H.408
- Hydrophobic interactions: A:L.607, A:L.607
- pi-Stacking: A:F.637
- 4 x DW3: 2-oxidanylethanal(Non-covalent)
DW3.5: 4 residues within 4Å:- Chain A: Y.245, H.246, S.269
- Ligands: DW3.7
1 PLIP interactions:1 interactions with chain A- Water bridges: A:N.267
DW3.6: 7 residues within 4Å:- Chain A: Q.633, F.634, F.637, H.677
- Chain B: F.342
- Ligands: TPP.10, DW3.11
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.633
DW3.7: 7 residues within 4Å:- Chain A: F.342
- Chain B: Q.633, F.634, F.637, H.677
- Ligands: TPP.4, DW3.5
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.633
DW3.11: 6 residues within 4Å:- Chain A: H.677
- Chain B: Y.245, H.246, P.268, S.269
- Ligands: DW3.6
2 PLIP interactions:2 interactions with chain B- Water bridges: B:N.267, B:N.267
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Seo, P.W. et al., Understanding the molecular properties of the E1 subunit (SucA) of alpha-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin. Catalysis Science And Technology (2020)
- Release Date
- 2020-08-05
- Peptides
- Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.28 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
- 4 x DW3: 2-oxidanylethanal(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Seo, P.W. et al., Understanding the molecular properties of the E1 subunit (SucA) of alpha-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin. Catalysis Science And Technology (2020)
- Release Date
- 2020-08-05
- Peptides
- Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B