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Crystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in complex with ferric heme and mmg-0358
Analyse Crystal structure of indoleamine 2,3-dioxygenase 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
- 6R63
- Type
- protein
- Length
- 744 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
- JTB, HEM
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 371 | 58% helix, 5% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 373 | 60% helix, 3% strand | P14902 |
Ligands and binding sites
- JTB · 4-chloranyl-2-(2~{H}-1,2,3-triazol-4-yl)phenol · ligand · 3 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.84 | 0.85 | 118 | empty |
| 2 | 631 | 0.84 | 0.88 | 54 | HEM, JTB |
| 3 | 708 | 0.81 | 0.84 | 51 | HEM, JTB |
| 4 | 122 | 0.51 | 0.81 | 23 | empty |
| 5 | 80 | 0.44 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6R63 · Crystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in complex with ferric heme and… · the same entry in another collection · chain A against A, TM-score 1.00
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 6R63 · PDBe 6R63 · UniProt P14902
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