SMTL ID : 5yak.3 (2 other biounits)

The crystal structure of human IYD Thr239 mutant with ligand 3-Fluorotyrosine (F-Tyr)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: R.69, R.70, S.71, R.73, L.145, T.147, V.205, T.206, T.207, A.208, L.246, R.248 Chain B: P.96, S.97, G.98, H.100, Y.181, I.184, S.185 Ligands: YOF.2 21 PLIP interactions: 6 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:P.96, B:Y.181, B:Y.181, B:I.184 Hydrogen bonds: B:S.97, B:H.100, A:S.71, A:S.71, A:S.71, A:S.71, A:R.73, A:A.208 Water bridges: A:R.70, A:R.70, A:R.70, A:K.151, A:R.248, A:R.248 Salt bridges: A:R.69, A:R.70, A:R.248 FMN.3: 21 residues within 4Å: Chain A: P.96, S.97, G.98, A.99, H.100, Y.181, I.184, S.185 Chain B: R.69, R.70, S.71, R.73, L.145, T.147, V.205, T.206, T.207, A.208, L.246, R.248 Ligands: YOF.4 23 PLIP interactions: 6 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:P.96, A:Y.181, A:I.184, B:T.206 Hydrogen bonds: A:S.97, A:A.99, A:H.100, B:S.71, B:S.71, B:S.71, B:S.71, B:R.73, B:A.208 Water bridges: B:R.69, B:R.70, B:R.70, B:K.151, B:Y.153, B:R.248, B:R.248 Salt bridges: B:R.69, B:R.70, B:R.248

2 x YOF: 3-FLUOROTYROSINE(Non-covalent)

YOF.2: 13 residues within 4Å: Chain A: E.126, Y.130, W.138, L.142, L.145, T.147, N.148, K.151, A.208 Chain B: G.98, A.99, Y.181 Ligands: FMN.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.142, A:L.142, A:L.145 Hydrogen bonds: A:E.126, A:E.126, B:A.99 Water bridges: A:E.126, A:E.126, A:L.210 Salt bridges: A:K.151 YOF.4: 13 residues within 4Å: Chain A: G.98, A.99, Y.181 Chain B: E.126, Y.130, W.138, L.142, L.145, T.147, N.148, K.151, A.208 Ligands: FMN.3 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.142, B:L.142, B:L.145 Hydrogen bonds: B:E.126, B:Y.130, B:Y.130, B:T.147, A:A.99 Water bridges: B:N.129 Salt bridges: B:K.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, J. et al., Redox control of iodotyrosine deiodinase. Protein Sci. (2019)

Release Date

2018-08-08

Peptides

Iodotyrosine deiodinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

Iodotyrosine deiodinase 1

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