SMTL ID : 4zad.1

Structure of C. dubliensis Fdc1 with the prenylated-flavin cofactor in the iminium form.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: N.174, H.197, E.240 Ligands: K.2, 4LU.3 4 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.240, H2O.1, H2O.1, 4LU.3 MN.4: 5 residues within 4Å: Chain B: N.174, H.197, E.240 Ligands: K.5, 4LU.6 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.197, B:E.240, H2O.3, H2O.3, 4LU.6

2 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: W.175, V.229, S.230, M.232, E.240 Ligands: MN.1, 4LU.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:M.232, 4LU.3 K.5: 7 residues within 4Å: Chain B: W.175, V.229, S.230, M.232, E.240 Ligands: MN.4, 4LU.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:V.229, B:M.232, B:E.240, 4LU.6

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.3: 23 residues within 4Å: Chain A: T.159, N.174, W.175, S.176, I.177, A.178, R.179, L.191, Q.196, H.197, S.230, S.231, M.232, P.233, E.240, E.289, S.321, P.323, T.330, I.334, K.405 Ligands: MN.1, K.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.177, A:I.177, A:R.179, A:P.323, A:T.330, A:I.334 Hydrogen bonds: A:N.174, A:I.177, A:I.177, A:R.179, A:Q.196, A:H.197, A:S.231, A:E.289, A:K.405 Water bridges: A:S.176, A:L.191, A:V.198 Salt bridges: A:H.197, A:K.405 4LU.6: 22 residues within 4Å: Chain B: T.159, N.174, S.176, I.177, A.178, R.179, L.191, Q.196, H.197, S.230, S.231, M.232, P.233, E.240, E.289, S.321, P.323, T.330, I.334, K.405 Ligands: MN.4, K.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.177, B:I.177, B:R.179, B:P.323, B:T.330, B:I.334 Hydrogen bonds: B:N.174, B:I.177, B:I.177, B:R.179, B:Q.196, B:H.197, B:S.231 Water bridges: B:I.234, B:K.405 Salt bridges: B:H.197, B:K.405

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
B

Fdc1