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Crystal structure of the indoleamine 2,3-dioxygenase 1 (IDO1) in complexed with ferric heme and epacadostat
Analyse Crystal structure of the indoleamine 2,3-dioxygenase 1 (IDO1) in complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E40
- Type
- protein
- Length
- 1,486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indoleamine 2,3-dioxygenase 1
- EC
- 1.13.11.52
- UniProt
- P14902
- Ligands
- HEM, BBJ
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 370 | 61% helix, 4% strand | P14902 |
| B, C | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 369 | 61% helix, 3% strand | P14902 |
| D | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 378 | 62% helix, 4% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- BBJ · N-(3-bromo-4-fluorophenyl)-N'-hydroxy-4-{[2-(sulfamoylamino)ethyl]amino}-1,2,5-oxadiazole-3-carboximidamide · ligand · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.81 | 0.82 | 79 | HEM, BBJ |
| 2 | 780 | 0.80 | 0.83 | 61 | HEM, BBJ |
| 3 | 773 | 0.79 | 0.82 | 65 | HEM |
| 4 | 756 | 0.79 | 0.82 | 70 | HEM, BBJ |
| 5 | 845 | 0.75 | 0.79 | 70 | empty |
Interfaces
3 interfaces between chains.
- C–D · 615 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 604 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 52 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6E40 · Crystal structure of the indoleamine 2,3-dioxygenase 1 (IDO1) in complexed with ferric… · the same entry in another collection · chain A against A, TM-score 1.00
- P14902 · AlphaFold monomer V2.0 prediction for indoleamine 2,3-dioxygenase 1 (P14902) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P14902
- Elsewhere: RCSB PDB 6E40 · PDBe 6E40 · UniProt P14902
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