SMTL ID : 3iaf.1

Structure of benzaldehyde lyase A28S mutant with monomethyl benzoylphosphonate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 26 residues within 4Å: Chain A: A.394, L.395, T.396, G.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, A.480, T.481 Chain B: L.25, H.26, E.50, T.73, G.76, G.77, N.80, Q.113 Ligands: MG.2 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.394, A:L.395, A:T.396, A:T.396, A:G.419, A:M.421, A:D.448, A:G.449, A:S.450, A:N.475, A:G.479, A:A.480 Hydrophobic interactions: B:T.73 TPP.3: 29 residues within 4Å: Chain A: L.25, H.26, G.27, S.28, E.50, T.73, G.76, G.77, N.80, Q.113 Chain B: G.393, A.394, L.395, T.396, G.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, A.480, T.481 Ligands: MG.4 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.478, B:W.478, A:L.25, A:T.73 Hydrogen bonds: B:A.394, B:L.395, B:T.396, B:T.396, B:T.396, B:G.419, B:M.421, B:D.448, B:G.449, B:S.450, B:N.475, B:G.479, B:A.480 Water bridges: A:Q.113, A:Q.113 TPP.5: 27 residues within 4Å: Chain C: G.393, A.394, L.395, T.396, G.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, A.480, T.481 Chain D: H.26, G.27, S.28, E.50, T.73, G.76, N.80, Q.113 Ligands: MG.6 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.453, D:T.73 Hydrogen bonds: C:L.395, C:T.396, C:T.396, C:G.419, C:M.421, C:G.449, C:S.450, C:Y.453, C:N.475, C:G.479, C:A.480 Water bridges: D:Q.113, D:Q.113 TPP.7: 28 residues within 4Å: Chain C: H.26, G.27, S.28, E.50, T.73, G.76, G.77, N.80, Q.113 Chain D: G.393, A.394, L.395, T.396, G.419, S.420, M.421, G.447, D.448, G.449, S.450, Y.453, N.475, S.477, W.478, G.479, A.480, T.481 Ligands: MG.8 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:W.478, D:W.478, C:T.73 Hydrogen bonds: D:L.395, D:T.396, D:T.396, D:G.419, D:M.421, D:G.449, D:S.450, D:Y.453, D:N.475, D:G.479, D:A.480 Water bridges: C:G.77, C:Q.113

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.448, M.473, N.475, S.477 Ligands: TPP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.448, A:S.477 MG.4: 6 residues within 4Å: Chain B: G.447, D.448, M.473, N.475, S.477 Ligands: TPP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.448, B:S.477 MG.6: 6 residues within 4Å: Chain C: G.447, D.448, M.473, N.475, S.477 Ligands: TPP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.448, C:S.477 MG.8: 6 residues within 4Å: Chain D: D.448, G.449, M.473, N.475, S.477 Ligands: TPP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.448, D:S.477

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brandt, G.S. et al., Active-site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition. J.Am.Chem.Soc. (2010)

Release Date

2010-03-02

Peptides

Benzaldehyde lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Benzaldehyde lyase

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