MolNFT v1 · #160942 · protein
Crystal structure of human tryptophan 2,3-dioxygenase in complex with pf-06840003 in active site and exo site
6PYY: “Crystal structure of human tryptophan 2,3-dioxygenase in complex with pf-06840003 in active site and exo site”. X-ray diffraction, 2 ligands (H7S, HEM), 20 pockets (best druggability 0.90). MolNFT v1 #160942 on GenesisL1: 3D…
- PDB
- 6PYY
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan 2,3-dioxygenase
- EC
- 1.13.11.11
- UniProt
- P48775
- Ligands
- H7S, HEM
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 351 | 72% helix, 0% strand | P48775 |
| B | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 342 | 68% helix, 0% strand | P48775 |
| C | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 332 | 67% helix, 0% strand | P48775 |
| D | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 347 | 71% helix, 1% strand | P48775 |
Ligands and binding sites
- H7S · (3S)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione · ligand · 8 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.90 | 0.92 | 156 | empty |
| 2 | 387 | 0.86 | 0.95 | 47 | HEM, H7S |
| 3 | 385 | 0.86 | 0.94 | 39 | HEM, H7S |
| 4 | 404 | 0.86 | 0.94 | 45 | HEM, H7S |
| 5 | 565 | 0.77 | 0.83 | 51 | HEM, H7S |
Interfaces
6 interfaces between chains.
- C–D · 2966 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2941 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 1933 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1885 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 840 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6PYY · Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PF-06840003 in… · the same entry in another collection · chain B against B, 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 P48775
- Elsewhere: RCSB PDB 6PYY · PDBe 6PYY · UniProt P48775
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