SMTL ID : 8y7s.3 (2 other biounits)

Crystal structure of a benzaldehyde lyase mutant M6 from Herbiconiux sp. SALV-R1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 28 residues within 4Å: Chain A: G.391, A.392, L.393, T.394, S.417, S.418, M.419, G.443, D.444, G.445, A.446, Y.449, N.471, A.473, W.474, G.475, A.476, T.477 Chain B: I.24, N.25, G.26, E.49, T.72, G.75, G.76, N.79, Q.112 Ligands: MG.2 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.474, A:W.474, A:T.477, B:I.24, B:T.72 Hydrogen bonds: A:A.392, A:L.393, A:T.394, A:T.394, A:S.417, A:M.419, A:G.445, A:A.446, A:N.471, A:G.475, A:A.476 TPP.3: 28 residues within 4Å: Chain A: I.24, N.25, G.26, E.49, T.72, G.75, G.76, N.79, Q.112 Chain B: G.391, A.392, L.393, T.394, S.417, S.418, M.419, G.443, D.444, G.445, A.446, Y.449, N.471, A.473, W.474, G.475, A.476, T.477 Ligands: MG.4 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.474, B:W.474, B:T.477, A:I.24, A:T.72 Hydrogen bonds: B:A.392, B:L.393, B:T.394, B:T.394, B:S.417, B:M.419, B:D.444, B:G.445, B:A.446, B:N.471, B:A.473, B:G.475, B:A.476 Water bridges: A:Q.112 TPP.5: 27 residues within 4Å: Chain C: G.391, A.392, L.393, T.394, S.417, S.418, M.419, G.443, D.444, G.445, A.446, Y.449, N.471, A.473, W.474, G.475, A.476, T.477 Chain D: I.24, N.25, E.49, T.72, G.75, G.76, N.79, Q.112 Ligands: MG.6 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.474, C:W.474, C:T.477, D:I.24 Hydrogen bonds: C:A.392, C:L.393, C:T.394, C:S.417, C:M.419, C:G.445, C:A.446, C:Y.449, C:N.471, C:G.475, C:A.476 Water bridges: C:D.444, C:N.471 TPP.7: 26 residues within 4Å: Chain C: N.25, E.49, T.72, G.75, G.76, N.79, Q.112 Chain D: G.391, A.392, L.393, T.394, S.417, S.418, M.419, G.443, D.444, G.445, A.446, Y.449, N.471, A.473, W.474, G.475, A.476, T.477 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.474, D:W.474, D:T.477 Hydrogen bonds: D:A.392, D:L.393, D:T.394, D:S.417, D:M.419, D:G.445, D:A.446, D:G.475, D:A.476

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.444, N.471, A.473 Ligands: TPP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.444, A:A.473 MG.4: 4 residues within 4Å: Chain B: D.444, N.471, A.473 Ligands: TPP.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.444, B:D.444, B:A.473 MG.6: 5 residues within 4Å: Chain C: D.444, N.471, A.473, G.475 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.444, C:A.473, H2O.4 MG.8: 4 residues within 4Å: Chain D: D.444, N.471, A.473 Ligands: TPP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.444, D:A.473

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Manipulating Activity and Chemoselectivity of a Benzaldehyde Lyase for Efficient Synthesis of alpha-Hydroxymethyl Ketones and One-Pot Enantio-Complementary Conversion to 1,2-Diols. Acs Catalysis (2024)

Release Date

2025-02-12

Peptides

Thiamine pyrophosphate-binding protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
L

C
G

D
I

Thiamine pyrophosphate-binding protein

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