SMTL ID : 8y7s.1 (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 C: I.24, N.25, G.26, E.49, T.72, G.75, G.76, N.79, Q.112 Ligands: MG.2 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.392, A:L.393, A:T.394, A:T.394, A:S.417, A:M.419, A:D.444, A:G.445, A:A.446, A:N.471, A:G.475, A:A.476 Water bridges: A:N.471 Hydrophobic interactions: C:I.24, C:T.72 TPP.3: 27 residues within 4Å: 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 Chain D: N.25, I.27, E.49, T.72, G.75, G.76, N.79, Q.112 Ligands: MG.4 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:W.474, B:W.474, B:T.477 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:G.475, B:A.476 Water bridges: B:S.417, D:G.76, D:Q.112 TPP.5: 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 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 Ligands: MG.6 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:W.474, C:W.474, C:T.477, A:T.72 Hydrogen bonds: C:A.392, C:L.393, C:T.394, C:T.394, C:S.417, C:M.419, C:G.445, C:A.446, C:Y.449, C:G.475, C:A.476 Water bridges: A:G.76, A:Q.112 TPP.7: 27 residues within 4Å: Chain B: I.24, 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 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:W.474, D:W.474, B:I.24, B:T.72 Hydrogen bonds: D:A.392, D:L.393, D:T.394, D:S.417, D:M.419, D:G.445, D:A.446, D:N.471, D:G.475, D:A.476 Water bridges: B:Q.112

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.444, N.471, A.473, G.475 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.444, A:A.473, H2O.1 MG.4: 4 residues within 4Å: Chain B: D.444, N.471, A.473 Ligands: TPP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: 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 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.444, C:A.473 MG.8: 5 residues within 4Å: Chain D: G.443, 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
A

B
B

C
E

D
F

Thiamine pyrophosphate-binding protein

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