SMTL ID : 6ev4.1

Structure of wild type A. niger Fdc1 purified in the dark with prFMN in the iminium form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.14 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: 22 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 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.171, A:I.171, A:R.173, A:E.322, A:T.323, A:I.327 Hydrogen bonds: A:N.168, 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:K.391, A:K.391 Salt bridges: A:H.191, A:K.391 4LU.5: 22 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.6, K.7 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.171, B:I.171, B:R.173, B:E.322, B:T.323, B:I.327 Hydrogen bonds: B:N.168, 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: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.3, H2O.9 MN.6: 5 residues within 4Å: Chain B: N.168, H.191, E.233 Ligands: 4LU.5, K.7 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.5, H2O.36, H2O.42

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: 5 residues within 4Å: Chain A: R.421, D.427, D.459, L.461 Chain B: N.447 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.14 K.7: 7 residues within 4Å: Chain B: W.169, A.222, S.223, M.225, E.233 Ligands: 4LU.5, MN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.222, B:M.225, B:E.233, 4LU.5 K.8: 5 residues within 4Å: Chain A: N.447 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.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bailey, S.S. et al., The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis. J. Biol. Chem. (2018)

Release Date

2017-12-27

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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