Research workbench
Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) in complex with compound 36
Analyse Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KPS
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.249
- Source
- Homo sapiens
- Molecule
- Indoleamine 2,3-dioxygenase 1
- EC
- 1.13.11.52
- UniProt
- P14902
- Ligands
- HEM, DU6
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.249 · 2 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 | 370 | 62% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 373 | 62% helix, 3% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- DU6 · 1-(4-cyanophenyl)-3-[[3-(2-cyclopropylethynyl) imidazo[2,1-b][1,3]thiazol-5-yl]methyl]urea · 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 | 1143 | 0.85 | 0.86 | 111 | HEM, DU6 |
| 2 | 711 | 0.81 | 0.84 | 59 | HEM, DU6 |
| 3 | 885 | 0.78 | 0.81 | 85 | empty |
| 4 | 59 | 0.39 | 0.80 | 18 | empty |
| 5 | 72 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 719 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6KPS · Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) in complex with compound 36 · 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 6KPS · PDBe 6KPS · UniProt P14902
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