Research workbench
Crystal structure of tryptophan 2,3-dioxygenase (tdo) from xanthomonas campestris in complex with ferrous heme and 6-fluoro-tryptophan. northeast structural genomics target XCR13
Analyse Crystal structure of tryptophan 2,3-dioxygenase (tdo) from xanthomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NW9
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan 2,3-dioxygenase
- UniProt
- Q8PDA8
- Ligands
- HEM, FT6, MN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan 2,3-dioxygenase | protein | 265 | 66% helix, 0% strand | Q8PDA8 |
| B | Tryptophan 2,3-dioxygenase | protein | 269 | 65% helix, 1% strand | Q8PDA8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- FT6 · 6-fluoro-L-tryptophan · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.84 | 0.90 | 53 | FT6, HEM |
| 2 | 495 | 0.77 | 0.84 | 54 | HEM |
| 3 | 180 | 0.51 | 0.78 | 27 | empty |
| 4 | 106 | 0.41 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3007 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 2NW9 · Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PDA8 · AlphaFold monomer V2.0 prediction for tryptophan 2,3-dioxygenase (Q8PDA8) · a predicted model of the same protein · chain A 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 Q8PDA8
- Elsewhere: RCSB PDB 2NW9 · PDBe 2NW9 · UniProt Q8PDA8
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