SMTL ID : 4za4.1

Structure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium form.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.22 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: 21 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, T.323, I.327, K.391 Ligands: MN.2, K.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.171, A:I.171, A:R.173, A:I.327, 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:L.185, A:I.192, A:K.391, A:K.391 Salt bridges: A:H.191, A:K.391 4LU.5: 21 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, T.323, I.327, K.391 Ligands: MN.6, K.7 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.171, B:I.171, B:R.173, B:I.327, 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:L.185, B:I.192, 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.4 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.19, H2O.21

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.28 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: 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.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Payne, K.A. et al., New cofactor supports alpha , beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature (2015)

Release Date

2015-06-17

Peptides

Fdc1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Fdc1

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