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Crystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) free enzyme in the ferrous state
Analyse Crystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) free enzyme in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E45
- Type
- protein
- Length
- 1,480 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, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 368 | 62% helix, 3% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 373 | 62% helix, 3% strand | P14902 |
| C | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 370 | 62% helix, 3% strand | P14902 |
| D | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 369 | 61% helix, 3% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains B, A, D, C
- GOL · Glycerol · additive · 5 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.78 | 0.82 | 53 | HEM, GOL |
| 2 | 625 | 0.78 | 0.83 | 51 | HEM |
| 3 | 628 | 0.78 | 0.83 | 49 | HEM, GOL |
| 4 | 709 | 0.77 | 0.82 | 56 | HEM |
| 5 | 589 | 0.71 | 0.79 | 84 | PO4, GOL |
Interfaces
5 interfaces between chains.
- A–B · 549 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 327 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 254 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 138 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 73 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6E45 · CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) free enzyme in the… · the same entry in another collection · chain D against D, 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 D 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 6E45 · PDBe 6E45 · UniProt P14902
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