MolNFT v1 · #160943 · protein
Crystal structure of human tryptophan 2,3-dioxygenase in complex with pf-06840003 in active site
6PYZ: “Crystal structure of human tryptophan 2,3-dioxygenase in complex with pf-06840003 in active site”. X-ray diffraction, 3 ligands (HEM, H7S, ZIQ), 20 pockets (best druggability 0.88). MolNFT v1 #160943 on GenesisL1: 3D structure…
- PDB
- 6PYZ
- Type
- protein
- Length
- 1,376 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
- HEM, H7S, ZIQ
- Pockets
- 20 · best druggability 0.88
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 | 353 | 70% helix, 0% strand | P48775 |
| B | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 348 | 69% helix, 0% strand | P48775 |
| C | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 333 | 70% helix, 0% strand | P48775 |
| D | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 342 | 73% helix, 1% strand | P48775 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- H7S · (3S)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione · ligand · 4 copies · chains A, B, C, D
- ZIQ · alpha-methyl-L-tryptophan · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.88 | 0.92 | 86 | empty |
| 2 | 383 | 0.86 | 0.94 | 43 | HEM, H7S |
| 3 | 374 | 0.86 | 0.94 | 47 | HEM, H7S |
| 4 | 433 | 0.85 | 0.92 | 45 | HEM, H7S |
| 5 | 356 | 0.83 | 0.92 | 64 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2957 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2913 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 1958 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1815 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 863 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6PYZ · Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PF-06840003 in… · the same entry in another collection · chain D against D, TM-score 1.00
- P48775 · AlphaFold monomer V2.0 prediction for tryptophan 2,3-dioxygenase (P48775) · a predicted model of the same protein · chain D 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 P48775
- Elsewhere: RCSB PDB 6PYZ · PDBe 6PYZ · UniProt P48775
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