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Structure of the S167H mutant of human indoleamine 2,3 dioxygenase in complex with tryptophan and cyanide
Analyse Structure of the S167H mutant of human indoleamine 2,3 dioxygenase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CXU
- 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
- 8 · best druggability 0.90
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 | 59% 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.90 | 0.91 | 133 | HEM, CYN, TRP |
| 2 | 450 | 0.87 | 0.94 | 49 | HEM, CYN, TRP |
| 3 | 56 | 0.48 | 0.85 | 15 | empty |
| 4 | 160 | 0.47 | 0.77 | 30 | empty |
| 5 | 148 | 0.46 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 688 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6CXU · Structure of the S167H mutant of human indoleamine 2,3 dioxygenase in complex with… · 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 6CXU · PDBe 6CXU · UniProt P14902
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