SMTL ID : 7p0n.3 (3 other biounits)

Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the open conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 22 residues within 4Å: Chain A: Y.128, F.165, S.169, V.172, F.216, I.219, F.228, A.266, G.267, F.272, F.293, L.294, R.345, H.348, I.351, V.352, I.356, L.386, F.389, L.390, V.393 Ligands: TRP.3 20 PLIP interactions: 15 interactions with chain A, 5 Ligand-Ligand interactions Hydrophobic interactions: A:F.165, A:V.172, A:F.216, A:I.219, A:F.228, A:A.266, A:F.272, A:I.351, A:V.352, A:I.356, A:L.386, A:F.389, W.3, W.3 Hydrogen bonds: A:G.267 Salt bridges: A:R.345 Metal complexes: A:H.348 Water bridges: W.3, W.3 pi-Stacking: W.3

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

NFK.2: 4 residues within 4Å: Chain A: L.213, H.217, Y.347, Q.350 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.347 Water bridges: A:H.217 Salt bridges: A:H.217

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 9 residues within 4Å: Chain A: F.228, R.233, G.263, G.264, S.265, A.266, I.356 Ligands: HEM.1, GOL.8 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.228, A:A.266 Hydrogen bonds: A:G.263, A:S.265 Water bridges: A:R.233, A:S.237 Salt bridges: A:R.233

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: H.18, L.27, P.28, K.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.75 Salt bridges: A:H.18

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: K.46, L.153, S.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.46, A:K.46, A:K.46, A:S.155 GOL.6: 3 residues within 4Å: Chain A: E.32, N.33, K.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.32, A:N.33, A:N.33 GOL.7: 6 residues within 4Å: Chain A: C.114, S.117, A.118, L.122, P.123, W.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.122 GOL.8: 7 residues within 4Å: Chain A: S.237, G.238, K.240, N.242, A.262, G.263 Ligands: TRP.3 7 PLIP interactions: 5 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.238, A:K.240, A:N.242, A:G.263 Water bridges: A:S.237, W.3, W.3 GOL.9: 4 residues within 4Å: Chain A: V.101, R.102, K.103, V.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.101, A:K.103, A:V.104 GOL.10: 2 residues within 4Å: Chain A: L.203, E.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.204 GOL.11: 2 residues within 4Å: Chain A: Y.147, H.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.221, A:H.222, A:H.222

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

CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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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