MolNFT v1 · #117835 · protein
Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919 analogue
5EK3 · Indoleamine 2,3-dioxygenase 1: “Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919 analogue”. X-ray diffraction, 2 ligands (HEM, 5PK), 5 pockets (best druggability 0.87). MolNFT v1 #117835 on…
- PDB
- 5EK3
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- 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, 5PK
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 374 | 60% helix, 3% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 378 | 60% helix, 3% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 5PK · (1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.87 | 0.88 | 122 | HEM, 5PK |
| 2 | 779 | 0.81 | 0.84 | 59 | HEM, 5PK |
| 3 | 477 | 0.79 | 0.87 | 75 | empty |
| 4 | 76 | 0.46 | 0.82 | 19 | empty |
| 5 | 70 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 704 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5EK3 · Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919… · 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 A 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 5EK3 · PDBe 5EK3 · UniProt P14902
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