SMTL ID : 7p0r.3 (3 other biounits)

Crystal structure of L-Trp/Indoleamine 2,3-dioxygenase (hIDO1) complex with the JK-loop refined in the intermediate conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 22 residues within 4Å: Chain A: Y.128, F.165, S.169, V.172, F.216, I.219, F.228, S.265, A.266, G.267, F.272, F.293, L.294, R.345, H.348, I.351, V.352, Y.355, I.356, L.386, L.390, V.393 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.165, A:V.172, A:F.216, A:I.219, A:F.228, A:A.266, A:F.272, A:F.293, A:I.351, A:V.352, A:Y.355, A:I.356, A:L.386, A:L.390 Hydrogen bonds: A:S.265 Salt bridges: A:R.345 Metal complexes: A:H.348

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: K.46, L.153, F.154, S.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.46, A:S.155, A:S.155 GOL.3: 5 residues within 4Å: Chain A: Y.147, K.163, D.221, H.222 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.147, A:K.163, A:D.221 GOL.4: 5 residues within 4Å: Chain A: D.221, H.222, V.223, N.224 Ligands: GOL.3 No protein-ligand interaction detected (PLIP) GOL.5: 5 residues within 4Å: Chain A: S.117, E.121, L.122, P.123, P.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.117 GOL.6: 3 residues within 4Å: Chain A: H.217, Q.218, D.221 No protein-ligand interaction detected (PLIP)

1 x NFK: N'-Formylkynurenine(Non-covalent)

NFK.7: 10 residues within 4Å: Chain A: L.51, I.52, G.55, Q.56, L.57, R.58, G.95, K.96, D.100, R.102 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.57, A:K.96 Hydrogen bonds: A:R.58, A:K.96 Water bridges: A:E.62, A:H.98, A:R.102 Salt bridges: A:R.102 pi-Cation interactions: A:R.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mirgaux, M. et al., Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site. Int J Tryptophan Res (2021)

Release Date

2021-12-29

Peptides

Indoleamine 2,3-dioxygenase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Indoleamine 2,3-dioxygenase 1

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