MolNFT v1 · #172552 · protein
Structure of human indoleamine-2,3-dioxygenase 1 (HIDO1) with a complete jk loop
7A62 · Indoleamine 2,3-dioxygenase 1: “Structure of human indoleamine-2,3-dioxygenase 1 (HIDO1) with a complete jk loop”. X-ray diffraction, 2 ligands (HEM, CL), 16 pockets (best druggability 0.83). MolNFT v1 #172552 on GenesisL1: 3D…
- PDB
- 7A62
- Type
- protein
- Length
- 1,520 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, CL
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 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 | 374 | 61% helix, 4% strand | P14902 |
| B | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 378 | 61% helix, 4% strand | P14902 |
| C | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 393 | 58% helix, 3% strand | P14902 |
| D | Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52) | protein | 375 | 61% helix, 3% strand | P14902 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.83 | 0.85 | 72 | HEM |
| 2 | 721 | 0.81 | 0.84 | 62 | HEM |
| 3 | 719 | 0.81 | 0.84 | 67 | HEM |
| 4 | 670 | 0.79 | 0.84 | 56 | HEM |
| 5 | 254 | 0.49 | 0.73 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–C · 260 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 250 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 103 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7A62 · Structure of human indoleamine-2,3-dioxygenase 1 (hIDO1) with a complete JK loop · 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 7A62 · PDBe 7A62 · UniProt P14902
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