SMTL ID : 6e35.1

Crystal structure of human indoleamime 2,3-dioxygenase (IDO1) in complex with L-Trp and cyanide, Northeast Structural Genomics Target HR6160

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: 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.2, TRP.3, ZCW.4 25 PLIP interactions: 23 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:V.160, A:F.204, A:I.207, A:F.216, A:F.216, A:A.254, 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, A:T.372, W.3 Water bridges: A:R.333 Salt bridges: A:R.333 Metal complexes: A:H.336 pi-Stacking: W.3 HEM.5: 26 residues within 4Å: Chain B: 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.6, TRP.7 24 PLIP interactions: 21 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:V.160, B:F.204, B:I.207, B:A.254, B:F.260, B:F.260, B:I.339, B:V.340, B:Y.343, B:I.344, B:T.372, B:L.374, B:F.377, B:F.377 Hydrogen bonds: B:G.368, B:G.370, B:G.371, B:T.372, B:T.372, W.7, W.7 Salt bridges: B:R.333 Metal complexes: B:H.336 pi-Stacking: W.7

2 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 5 residues within 4Å: Chain A: S.253, A.254, H.336 Ligands: HEM.1, TRP.3 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: W.3, A:A.254 CYN.6: 4 residues within 4Å: Chain B: S.253, A.254 Ligands: HEM.5, TRP.7 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: W.7, B:A.254

2 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: HEM.1, CYN.2 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:Y.116, A:L.224, A:T.369 Hydrogen bonds: A:T.369 Salt bridges: A:R.221 pi-Stacking: A:F.153 TRP.7: 13 residues within 4Å: Chain B: Y.116, F.153, F.216, R.221, L.224, G.252, S.253, A.254, I.344, G.368, T.369 Ligands: HEM.5, CYN.6 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.116, B:L.224, B:T.369 Hydrogen bonds: B:T.369, W.7, W.7 Water bridges: B:S.157 Salt bridges: B:R.221 pi-Stacking: B: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.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.164, A:L.197, A:F.260, A:F.260, A:F.260, A:F.263, A:L.329, A:L.332, A:L.332 Hydrogen bonds: A:F.260 Water bridges: A:R.333, A:R.333, A:H.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Forouhar, F. et al., Crystal structure of human indoleamime 2,3-dioxygenase (IDO1) in complex with L-Trp and cyanide, Northeast Structural Genomics Target HR6160. To Be Published

Release Date

2018-07-25

Peptides

Indoleamine 2,3-dioxygenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Indoleamine 2,3-dioxygenase 1

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