MolNFT v1 · #147150 · protein
Crystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) in complex with ferrous heme and tryptophan
6E46: “Crystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) in complex with ferrous heme and tryptophan”. X-ray diffraction, 3 ligands (HEM, TRP, PO4), 20 pockets (best druggability 0.86). MolNFT v1 #147150 on GenesisL1: 3D…
- PDB
- 6E46
- Type
- protein
- Length
- 1,493 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, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 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 | 373 | 61% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 373 | 60% helix, 4% strand | P14902 |
| C | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 372 | 60% helix, 3% strand | P14902 |
| D | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 375 | 61% helix, 4% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- TRP · Tryptophan · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.86 | 0.94 | 49 | HEM, TRP |
| 2 | 404 | 0.86 | 0.94 | 44 | HEM, TRP |
| 3 | 412 | 0.86 | 0.94 | 45 | HEM, TRP |
| 4 | 413 | 0.86 | 0.94 | 45 | HEM, TRP |
| 5 | 874 | 0.75 | 0.79 | 66 | empty |
Interfaces
3 interfaces between chains.
- A–B · 594 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 543 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6E46 · CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) in complex with ferrous… · the same entry in another collection · chain D against D, 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 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 6E46 · PDBe 6E46 · UniProt P14902
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