Research workbench
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
- 5WMX
- Type
- protein
- Length
- 757 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
- 10 · best druggability 0.87
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 | 379 | 58% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 378 | 60% 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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.87 | 0.89 | 89 | CYN, HEM, TRP, ZCW |
| 2 | 1099 | 0.87 | 0.88 | 104 | CYN, HEM, TRP, ZCW |
| 3 | 340 | 0.69 | 0.82 | 32 | empty |
| 4 | 64 | 0.66 | 0.95 | 14 | empty |
| 5 | 99 | 0.51 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 774 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5WMX · 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 5WMX · PDBe 5WMX · UniProt P14902
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