Research workbench
Mapping the binding trajectory of a suicide inhibitor in human indoleamine 2,3-dioxygenase 1
Analyse Mapping the binding trajectory of a suicide inhibitor in human indoleamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MQ6
- Type
- protein
- Length
- 737 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, H7P
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 371 | 61% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 366 | 60% helix, 3% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- H7P · (2R)-N-(4-chlorophenyl)-2-[cis-4-(6-fluoroquinolin-4-yl)cyclohexyl]propanamide · ligand · chains B
- GOL · Glycerol · additive · 6 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.83 | 0.84 | 130 | empty |
| 2 | 630 | 0.81 | 0.85 | 53 | H7P, GOL |
| 3 | 597 | 0.78 | 0.83 | 51 | HEM, GOL |
| 4 | 56 | 0.28 | 0.74 | 17 | GOL |
| 5 | 53 | 0.27 | 0.73 | 16 | GOL |
Interfaces
1 interface between chains.
- A–B · 723 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6MQ6 · Mapping the binding trajectory of a suicide inhibitor in human indoleamine… · 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 6MQ6 · PDBe 6MQ6 · UniProt P14902
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