SMTL ID : 6r2t.1

Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with prFMN (purified in the radical form) and phenylpropiolic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-dimer

Ligands

2 x 4LU: 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol(Non-covalent)

4LU.1: 23 residues within 4Å: Chain A: T.153, N.168, W.169, S.170, I.171, A.172, R.173, L.185, Q.190, H.191, S.223, S.224, M.225, P.226, E.233, C.316, E.322, T.323, I.327, K.391 Ligands: MN.2, K.3, JQ8.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.171, A:I.171, A:R.173, A:E.322, A:T.323, A:I.327, A:I.327 Hydrogen bonds: A:I.171, A:I.171, A:R.173, A:Q.190, A:H.191, A:S.224 Water bridges: A:S.170, A:S.170, A:L.185, A:I.227, A:K.391, A:K.391 Salt bridges: A:H.191, A:K.391 4LU.6: 23 residues within 4Å: Chain B: T.153, N.168, W.169, S.170, I.171, A.172, R.173, L.185, Q.190, H.191, S.223, S.224, M.225, P.226, E.233, C.316, E.322, T.323, I.327, K.391 Ligands: MN.7, K.8, JQ8.10 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.171, B:I.171, B:R.173, B:E.322, B:T.323, B:I.327, B:I.327 Hydrogen bonds: B:I.171, B:I.171, B:R.173, B:Q.190, B:H.191, B:S.224 Water bridges: B:S.170, B:S.170, B:L.185, B:I.227, B:K.391, B:K.391 Salt bridges: B:H.191, B:K.391

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: N.168, H.191, E.233 Ligands: 4LU.1, K.3 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:H.191, A:E.233, 4LU.1, H2O.2, H2O.5 MN.7: 5 residues within 4Å: Chain B: N.168, H.191, E.233 Ligands: 4LU.6, K.8 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:H.191, B:E.233, 4LU.6, H2O.28, H2O.31

4 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: W.169, A.222, S.223, M.225, E.233 Ligands: 4LU.1, MN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.222, A:M.225, A:E.233, 4LU.1 K.4: 4 residues within 4Å: Chain A: R.421, D.427, D.459, L.461 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.421, A:D.427, A:D.459, A:L.461, H2O.11 K.8: 7 residues within 4Å: Chain B: W.169, A.222, S.223, M.225, E.233 Ligands: 4LU.6, MN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.222, B:M.225, B:E.233, 4LU.6 K.9: 4 residues within 4Å: Chain B: R.421, D.427, D.459, L.461 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:R.421, B:D.427, B:D.459, B:L.461, H2O.37

2 x JQ8: phenylpropiolic acid(Non-covalent)

JQ8.5: 11 residues within 4Å: Chain A: R.173, Q.190, F.280, E.282, M.283, I.327, Y.394, T.395, F.437, L.439 Ligands: 4LU.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.327, A:Y.394, A:T.395, A:L.439 Hydrogen bonds: A:M.283 Salt bridges: A:R.173 pi-Stacking: A:F.437 JQ8.10: 11 residues within 4Å: Chain B: R.173, Q.190, F.280, E.282, M.283, I.327, Y.394, T.395, F.437, L.439 Ligands: 4LU.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.327, B:Y.394, B:T.395, B:L.439 Hydrogen bonds: B:M.283 Salt bridges: B:R.173 pi-Stacking: B:F.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bailey, S.S. et al., Atomic description of an enzyme reaction dependent on reversible 1,3-dipolar cycloaddition. to be published

Release Date

2019-08-28

Peptides

Ferulic acid decarboxylase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ferulic acid decarboxylase 1

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