SMTL ID : 4s27.1

Crystal structure of Arabidopsis thaliana ThiC with bound aminoimidazole ribonucleotide, 5'-deoxyadenosine, L-methionine, Fe4S4 cluster and Fe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-dimer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 9 residues within 4Å: Chain A: W.470, C.502, M.504, C.505, C.510, S.511, M.512 Ligands: CL.6, MET.12 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.502, A:C.505, A:C.510 SF4.9: 9 residues within 4Å: Chain B: W.470, C.502, M.504, C.505, C.510, S.511, M.512 Ligands: MET.4, CL.14 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.502, B:C.505, B:C.510

2 x AIR: 5-AMINOIMIDAZOLE RIBONUCLEOTIDE(Non-covalent)

AIR.2: 19 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 Ligands: 5AD.3, MET.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.160, 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 Salt bridges: A:H.254, A:R.318 AIR.10: 19 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 Ligands: 5AD.11, MET.12 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.160, B:N.160, B:T.252, B:R.275, B:G.276, B:R.318, B:E.354, B:Y.381 Water bridges: B:Y.218, B:Y.218, B:D.315 Salt bridges: B:H.254, B:R.318

2 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.3: 14 residues within 4Å: Chain A: N.160, I.161, G.162, N.163, L.191, R.275, R.318, L.383, E.421, L.425, P.426 Chain B: M.504 Ligands: AIR.2, MET.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.160, A:G.162, A:R.275, A:R.275, A:E.421 Water bridges: A:G.162, A:G.162, A:T.193 5AD.11: 14 residues within 4Å: Chain A: M.504 Chain B: N.160, I.161, G.162, N.163, L.191, R.275, R.318, L.383, E.421, L.425, P.426 Ligands: AIR.10, MET.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.160, B:G.162, B:R.275, B:R.275, B:E.421 Water bridges: B:G.162, B:G.162, B:T.193

2 x MET: METHIONINE(Non-covalent)

MET.4: 13 residues within 4Å: Chain A: V.273, R.275, R.318, H.358, L.383, E.421, H.422 Chain B: C.505, S.511 Ligands: AIR.2, 5AD.3, FE2.5, SF4.9 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.318, A:H.358 MET.12: 13 residues within 4Å: Chain A: C.505, S.511 Chain B: V.273, R.275, R.318, H.358, L.383, E.421, H.422 Ligands: SF4.1, AIR.10, 5AD.11, FE2.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.421 Salt bridges: B:R.318, B:H.358

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

FE2.5: 3 residues within 4Å: Chain A: H.358, H.422 Ligands: MET.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.358, A:H.422, H2O.15, H2O.15 FE2.13: 3 residues within 4Å: Chain B: H.358, H.422 Ligands: MET.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.358, B:H.422, H2O.34, H2O.34

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: M.512 Chain B: H.422 Ligands: SF4.1 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: H.422 Chain B: M.512 Ligands: SF4.9 Ligand excluded by PLIP

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

BU1.7: 4 residues within 4Å: Chain A: R.237, I.241, I.303, Q.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.237 BU1.8: 7 residues within 4Å: Chain A: K.32, V.45, P.46, F.47, D.60, T.115, R.116 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.32, A:F.47 Hydrogen bonds: A:P.46 BU1.15: 4 residues within 4Å: Chain B: R.237, I.241, I.303, Q.306 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.237 BU1.16: 7 residues within 4Å: Chain B: K.32, V.45, P.46, F.47, D.60, T.115, R.116 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.32, B:F.47 Hydrogen bonds: B:P.46, B:D.60

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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