SMTL ID : 3gfd.1

Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (MIT)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: R.64, R.65, S.66, R.68, L.140, T.142, V.200, T.201, T.202, T.203, L.241, R.243 Chain B: P.91, S.92, G.93, A.94, H.95, Y.176, I.179, S.180 Ligands: IYR.2 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.203, B:Y.176, B:I.179 Hydrogen bonds: A:S.66, A:S.66, A:S.66, A:S.66, A:R.68, A:T.203, A:T.203, B:S.92, B:A.94, B:H.95 Water bridges: A:R.64, A:R.65, A:R.68, A:K.146, A:Y.148, A:R.243, A:R.243 Salt bridges: A:R.64, A:R.65, A:R.243 FMN.5: 22 residues within 4Å: Chain A: P.91, S.92, G.93, A.94, H.95, Y.176, I.179, S.180, I.183 Chain B: R.64, R.65, S.66, R.68, L.140, T.142, V.200, T.201, T.202, T.203, L.241, R.243 Ligands: IYR.6 24 PLIP interactions: 8 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:P.91, A:Y.176, A:Y.176, A:I.179, A:I.183, B:T.203 Hydrogen bonds: A:S.92, A:A.94, A:H.95, B:S.66, B:S.66, B:S.66, B:R.68, B:T.203 Water bridges: B:R.65, B:R.65, B:R.68, B:Y.148, B:R.243, B:R.243, B:R.243 Salt bridges: B:R.64, B:R.65, B:R.243

2 x IYR: 3-IODO-TYROSINE(Non-covalent)

IYR.2: 13 residues within 4Å: Chain A: E.121, Y.125, W.133, L.137, T.142, N.143, K.146, T.203 Chain B: G.93, A.94, Y.175, Y.176 Ligands: FMN.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.137, A:L.137 Hydrogen bonds: A:Y.125, A:Y.125, B:A.94 Water bridges: A:E.121, A:N.124, A:Y.148, A:T.203, A:T.203 Salt bridges: A:K.146 IYR.6: 15 residues within 4Å: Chain A: G.93, A.94, Y.175, Y.176 Chain B: E.121, Y.125, M.129, W.133, L.137, L.140, T.142, N.143, K.146, T.203 Ligands: FMN.5 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.137, B:L.137, B:L.140 Hydrogen bonds: B:Y.125, B:T.142, A:A.94 Water bridges: B:E.121, B:E.121, B:Y.148, B:T.203, B:T.203 Salt bridges: B:K.146

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: Y.175, Y.176 Chain B: W.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.176 Water bridges: A:N.177 GOL.4: 5 residues within 4Å: Chain A: T.43, R.44, Y.45, P.46, E.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.44 GOL.7: 4 residues within 4Å: Chain A: W.133, L.205 Chain B: Y.175, Y.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.176 Water bridges: B:N.177, B:N.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, S.R. et al., Crystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands. J.Biol.Chem. (2009)

Release Date

2009-05-12

Peptides

Iodotyrosine dehalogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Iodotyrosine dehalogenase 1

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