MolNFT v1 · #147116 · protein
Crystal structure of human indoleamime 2,3-dioxygenase (IDO1) in complex with L-TRP and cyanide, northeast structural genomics target HR6160
6E35 · Indoleamine 2,3-dioxygenase 1: “Crystal structure of human indoleamime 2,3-dioxygenase (IDO1) in complex with L-TRP and cyanide, northeast…”. X-ray diffraction, 4 ligands (HEM, TRP, ZCW), 7 pockets (best druggability 0.88). MolNFT…
- PDB
- 6E35
- Type
- protein
- Length
- 731 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 · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 365 | 63% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 366 | 62% 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 · chains A
- 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.88 | 0.89 | 119 | HEM, CYN, TRP, ZCW |
| 2 | 1092 | 0.88 | 0.89 | 118 | HEM, CYN, TRP |
| 3 | 77 | 0.73 | 0.97 | 16 | empty |
| 4 | 203 | 0.50 | 0.76 | 31 | empty |
| 5 | 237 | 0.49 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 807 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6E35 · Crystal structure of human indoleamime 2,3-dioxygenase (IDO1) in complex with L-Trp and… · the same entry in another collection · chain B against B, 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 6E35 · PDBe 6E35 · UniProt P14902
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