SMTL ID : 3d7k.1

Crystal structure of benzaldehyde lyase in complex with the inhibitor MBP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.448, N.475, S.477, G.479 Ligands: D7K.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.448, A:S.477, H2O.1 CA.3: 5 residues within 4Å: Chain B: D.448, N.475, S.477, G.479 Ligands: D7K.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.448, B:S.477, H2O.5 CA.5: 5 residues within 4Å: Chain C: D.448, N.475, S.477, G.479 Ligands: D7K.6 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.448, C:S.477, H2O.8 CA.7: 5 residues within 4Å: Chain D: D.448, N.475, S.477, G.479 Ligands: D7K.8 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.448, D:S.477, H2O.12

4 x D7K: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium(Non-covalent)

D7K.2: 31 residues within 4Å: Chain A: G.393, A.394, L.395, T.396, Y.397, 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, G.27, A.28, E.50, T.73, G.76, G.77, N.80, L.112, Q.113 Ligands: CA.1 24 PLIP interactions: 15 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:W.478, A:W.478, A:A.480, A:T.481, B:L.25, B:T.73, B:L.112 Hydrogen bonds: A:L.395, A:T.396, A:G.419, A:M.421, A:G.447, A:D.448, A:G.449, A:S.450, A:N.475, A:G.479, A:A.480, B:A.28, B:Q.113, B:Q.113 Water bridges: B:H.29, B:H.29, B:E.50 D7K.4: 29 residues within 4Å: Chain A: H.26, G.27, A.28, E.50, T.73, G.76, G.77, N.80, Q.113 Chain B: G.393, A.394, L.395, T.396, Y.397, 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: CA.3 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.478, B:W.478, A:T.73 Hydrogen bonds: B:L.395, B:T.396, B:G.419, B:M.421, B:D.448, B:G.449, B:S.450, B:Y.453, B:N.475, B:G.479, B:A.480, A:A.28, A:Q.113 Water bridges: A:H.29, A:H.29 D7K.6: 31 residues within 4Å: Chain C: G.393, A.394, L.395, T.396, Y.397, 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: L.25, H.26, G.27, A.28, E.50, T.73, G.76, G.77, N.80, L.112, Q.113 Ligands: CA.5 24 PLIP interactions: 16 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:W.478, C:W.478, C:A.480, C:T.481, D:L.25, D:T.73, D:L.112 Hydrogen bonds: C:L.395, C:T.396, C:T.396, C:G.419, C:M.421, C:G.447, C:D.448, C:G.449, C:S.450, C:N.475, C:G.479, C:A.480, D:A.28, D:Q.113, D:Q.113 Water bridges: D:H.29, D:H.29 D7K.8: 29 residues within 4Å: Chain C: H.26, G.27, A.28, E.50, T.73, G.76, G.77, N.80, Q.113 Chain D: G.393, A.394, L.395, T.396, Y.397, 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: CA.7 19 PLIP interactions: 14 interactions with chain D, 5 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:D.448, D:G.449, D:S.450, D:N.475, D:N.475, D:G.479, D:A.480, C:A.28, C:Q.113 Water bridges: C:H.29, C:H.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brandt, G.S. et al., Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester. Biochemistry (2008)

Release Date

2008-07-01

Peptides

Benzaldehyde lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Benzaldehyde lyase