SMTL ID : 6r32.1

Aspergillus niger ferrulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid (Int1')

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: N.168, H.191, E.233 Ligands: K.2, JQZ.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.191, A:E.233, H2O.3, H2O.6 MN.5: 5 residues within 4Å: Chain B: N.168, H.191, E.233 Ligands: K.6, JQZ.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.191, B:E.233, H2O.30, H2O.33

4 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: W.169, A.222, S.223, M.225, E.233 Ligands: MN.1, JQZ.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.222, A:M.225, A:E.233 K.3: 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.44 K.6: 7 residues within 4Å: Chain B: W.169, A.222, S.223, M.225, E.233 Ligands: MN.5, JQZ.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.222, B:M.225, B:E.233 K.7: 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.16

2 x JQZ: prFMN cofactor and phenylpropiolic acid(Non-covalent)

JQZ.4: 29 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, F.280, E.282, M.283, C.316, E.322, T.323, I.327, K.391, Y.394, T.395, F.437, L.439 Ligands: MN.1, K.2 28 PLIP interactions: 28 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:Y.394, A:T.395, A:F.437, A:F.437, A:L.439 Hydrogen bonds: A:N.168, A:I.171, A:I.171, A:R.173, A:Q.190, A:H.191, A:S.224, A:M.283 Water bridges: A:S.170, A:L.185, A:Q.190, A:I.192, A:I.227, A:K.391 Salt bridges: A:R.173, A:H.191, A:K.391 JQZ.8: 29 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, F.280, E.282, M.283, C.316, E.322, T.323, I.327, K.391, Y.394, T.395, F.437, L.439 Ligands: MN.5, K.6 28 PLIP interactions: 28 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:Y.394, B:T.395, B:F.437, B:F.437, B:L.439 Hydrogen bonds: B:N.168, B:I.171, B:I.171, B:R.173, B:Q.190, B:H.191, B:S.224, B:M.283 Water bridges: B:S.170, B:L.185, B:Q.190, B:I.192, B:I.227, B:K.391 Salt bridges: B:R.173, B:H.191, B:K.391

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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