SMTL ID : 6km9.1

Crystal structure of SucA from Vibrio vulnificus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-dimer

Ligands

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.1: 11 residues within 4Å: Chain A: G.248, F.249, S.250, A.263, L.264, A.265, F.266, V.277, S.281, M.474, R.658 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.250, A:F.266, A:S.281, A:R.658, A:R.658 P6G.5: 12 residues within 4Å: Chain B: G.248, F.249, S.250, A.263, L.264, A.265, F.266, V.277, S.281, M.474, T.621, R.658 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.250, B:S.281, B:R.658, B:R.658

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.305, N.338, V.340 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.305, A:V.340, H2O.1 MG.6: 4 residues within 4Å: Chain B: D.305, N.338, V.340 Ligands: TPP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.305, B:V.340

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 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, F.342, H.408 Chain B: Q.564, L.607, E.609, Q.633, F.637 Ligands: MG.2 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.270, B:L.607 Hydrogen bonds: A:S.269, A:L.271, A:D.305, A:S.306, A:A.307, A:N.338 Water bridges: A:R.209, A:R.209, A:G.304 Salt bridges: A:H.208, A:R.209, A:H.408 pi-Stacking: B:F.637 TPP.7: 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, F.342, H.408 Ligands: MG.6 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.342, A:Q.564, A:L.607 Hydrogen bonds: B:S.269, B:L.271, B:D.305, B:S.306, B:A.307, B:F.342 Water bridges: B:R.404 Salt bridges: B:H.208, B:R.209, B:H.408 pi-Stacking: A:F.637

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: E.610 Chain B: E.610 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.610, B:E.610

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
A

B
B

Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component

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