MolNFT v1 · #138556 · protein
Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase I
5WMU · Indoleamine 2,3-dioxygenase 1: “Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase I”. X-ray diffraction, 3 ligands (HEM, TRP, CYN), 9 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 5WMU
- Type
- protein
- Length
- 760 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, CYN
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 381 | 60% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 379 | 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
- 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.89 | 0.91 | 133 | HEM, CYN, TRP |
| 2 | 508 | 0.88 | 0.94 | 50 | HEM, CYN, TRP |
| 3 | 127 | 0.65 | 0.88 | 28 | empty |
| 4 | 152 | 0.48 | 0.78 | 29 | empty |
| 5 | 149 | 0.45 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 731 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5WMU · 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 5WMU · PDBe 5WMU · UniProt P14902
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