SMTL ID : 4s29.1

Crystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide and Fe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x IRN: 1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole(Non-covalent)

IRN.1: 17 residues within 4Å: Chain A: N.160, M.189, L.191, Y.218, T.252, H.254, S.274, R.275, G.276, D.315, R.318, E.354, G.355, Y.381, T.382, L.383, C.415 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.160, A:Y.218, A:R.275, A:G.276, A:R.318, A:E.354, A:E.354, A:Y.381 Water bridges: A:D.315, A:D.315 Salt bridges: A:H.254, A:R.318 pi-Stacking: A:Y.381 IRN.4: 17 residues within 4Å: Chain B: N.160, M.189, L.191, Y.218, T.252, H.254, S.274, R.275, G.276, D.315, R.318, E.354, G.355, Y.381, T.382, L.383, C.415 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.160, B:T.252, B:R.275, B:G.276, B:R.318, B:E.354 Water bridges: B:D.315, B:D.315 Salt bridges: B:H.254, B:R.318 pi-Stacking: B:Y.381

2 x FE2: FE (II) ION(Non-covalent)

FE2.2: 2 residues within 4Å: Chain A: H.358, H.422 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.358, A:H.422, H2O.10, H2O.10 FE2.5: 2 residues within 4Å: Chain B: H.358, H.422 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.358, B:H.422, H2O.30, H2O.31

2 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.3: 3 residues within 4Å: Chain A: R.237, I.241, Q.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.237 BU1.6: 3 residues within 4Å: Chain B: R.237, I.241, Q.306 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, M.K. et al., Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase. Nat Commun

Release Date

2015-04-08

Peptides

Phosphomethylpyrimidine synthase, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphomethylpyrimidine synthase, chloroplastic

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