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Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1
Analyse Structural insights into substrate and inhibitor binding sites in human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WMV
- Type
- protein
- Length
- 761 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, TRP, ZCW, CYN
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 381 | 58% helix, 3% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 380 | 59% helix, 4% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- ZCW · 2-(1H-indol-3-yl)ethanol · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.88 | 0.89 | 114 | CYN, HEM, TRP, ZCW |
| 2 | 557 | 0.88 | 0.93 | 50 | CYN, HEM, TRP, ZCW |
| 3 | 1169 | 0.76 | 0.79 | 109 | empty |
| 4 | 139 | 0.46 | 0.77 | 27 | empty |
| 5 | 146 | 0.43 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 856 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5WMV · Structural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine… · 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 B 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 5WMV · PDBe 5WMV · UniProt P14902
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