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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 4 residues within 4Å: Chain A: K.139, Y.147, E.148, K.163 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.147, A:E.148 Salt bridges: A:K.139 Hydrogen bonds: W.1, W.1

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: D.40, F.43, I.44, R.60 Ligands: GOL.3 No protein-ligand interaction detected (PLIP) GOL.3: 5 residues within 4Å: Chain A: D.40, K.63, L.64, N.65 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.40, A:N.65 GOL.4: 4 residues within 4Å: Chain A: C.161, D.221, H.222, N.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.222, A:N.224 Water bridges: A:N.224 GOL.5: 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:S.155, A:S.155, A:S.155 GOL.6: 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:K.103, A:V.104 Water bridges: A:V.101 GOL.7: 4 residues within 4Å: Chain A: N.29, Q.31, D.74, K.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.31 Water bridges: A:D.74, A:K.76 GOL.8: 6 residues within 4Å: Chain A: S.237, G.238, K.240, A.262, G.263, G.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.238, A:K.240, A:K.240 Water bridges: A:S.237, A:G.264 GOL.9: 4 residues within 4Å: Chain A: R.58, E.62, Y.92, R.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.92, A:R.102 Water bridges: A:E.59 GOL.10: 11 residues within 4Å: Chain A: V.277, L.278, L.279, G.280, L.312, E.313, N.315, P.316, S.317, V.318, R.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.278, A:E.313, A:V.318, A:R.319 GOL.11: 2 residues within 4Å: Chain A: R.195, G.329 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.195, A:R.195, A:G.329 Water bridges: A:D.196 GOL.12: 3 residues within 4Å: Chain A: S.314, N.315, P.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.315 GOL.13: 3 residues within 4Å: Chain A: P.258, K.259, E.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.258, A:E.260

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

HEM.14: 19 residues within 4Å: Chain A: F.165, S.169, F.216, I.219, F.228, A.266, G.267, F.272, F.293, R.345, H.348, I.351, V.352, Y.355, I.356, L.386, F.389, L.390, V.393 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:F.165, 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:F.389 Hydrogen bonds: A:G.267 Water bridges: A:R.233 Salt bridges: A:R.345 Metal complexes: A:H.348

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

CL.15: 2 residues within 4Å: Chain A: D.70, H.71 Ligand excluded by PLIP

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

PO4.16: 6 residues within 4Å: Chain A: G.280, I.281, Q.282, T.284, R.319, S.400 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.282, A:T.284, A:T.284 Water bridges: A:R.319 Salt bridges: A:R.319

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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