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Crystal structure of L-TRP/INDOLEAMINE 2,3-dioxygenase (HIDO1) complex with the jk-loop refined in the intermediate conformation
Analyse Crystal structure of L-TRP/INDOLEAMINE 2,3-dioxygenase (HIDO1) complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P0R
- Type
- protein
- Length
- 1,510 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, TRP, NFK, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 376 | 60% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 379 | 57% helix, 4% strand | P14902 |
| C | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 380 | 56% helix, 4% strand | P14902 |
| D | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 375 | 59% helix, 3% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- TRP · Tryptophan · ligand · 3 copies · chains B, A, D
- NFK · N'-Formylkynurenine · ligand · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 16 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.82 | 0.86 | 55 | HEM, TRP |
| 2 | 765 | 0.82 | 0.85 | 86 | HEM |
| 3 | 652 | 0.80 | 0.84 | 63 | HEM |
| 4 | 661 | 0.78 | 0.83 | 54 | HEM |
| 5 | 245 | 0.48 | 0.74 | 33 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 251 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 234 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 90 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 47 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme attachment).
Compared structures
- 7P0R · Crystal structure of L-Trp/Indoleamine 2,3-dioxygenase (hIDO1) complex with the JK-loop… · 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 0.98
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 7P0R · PDBe 7P0R · UniProt P14902
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