SMTL ID : 5wmv.1 (1 other biounit)

Structural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x CYN: CYANIDE ION(Non-covalent)

CYN.1: 5 residues within 4Å: Chain A: S.253, A.254, H.336 Ligands: HEM.2, TRP.3 3 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: W.3, W.3, A:A.254

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 28 residues within 4Å: Chain A: F.153, S.157, V.160, F.204, I.207, F.216, S.253, A.254, G.255, F.260, R.333, H.336, I.339, V.340, Y.343, I.344, G.368, T.369, G.370, G.371, T.372, L.374, F.377, L.378, V.381 Ligands: CYN.1, TRP.3, ZCW.4 28 PLIP interactions: 24 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:F.153, A:V.160, A:F.204, A:F.204, A:I.207, A:F.216, A:F.216, A:F.260, A:F.260, A:F.260, A:I.339, A:V.340, A:Y.343, A:L.374, A:F.377 Hydrogen bonds: A:G.368, A:T.369, A:G.370, A:G.371, A:T.372, W.3, W.3, W.3 Water bridges: A:D.264, A:R.333 Salt bridges: A:R.333 Metal complexes: A:H.336 pi-Stacking: W.3

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 14 residues within 4Å: Chain A: Y.116, C.119, F.153, F.216, R.221, L.224, G.252, S.253, A.254, I.344, G.368, T.369 Ligands: CYN.1, HEM.2 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.116, A:F.216, A:L.224, A:L.224 Hydrogen bonds: A:T.369, A:T.369, W.3 Salt bridges: A:R.221 pi-Stacking: A:F.153

1 x ZCW: 2-(1H-indol-3-yl)ethanol(Non-covalent)

ZCW.4: 9 residues within 4Å: Chain A: A.164, L.197, F.260, F.263, L.329, L.332, R.333, H.336 Ligands: HEM.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.164, A:L.197, A:F.260, A:F.263, A:L.329, A:L.332, A:L.332 Hydrogen bonds: A:F.260, A:H.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis-Ballester, A. et al., Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1. Nat Commun (2017)

Release Date

2017-12-06

Peptides

Indoleamine 2,3-dioxygenase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Indoleamine 2,3-dioxygenase 1

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