MolNFT v1 · #58994 · protein
H55A mutant of tryptophan 2,3-dioxygenase from xanthomonas campestris
3BK9: “H55A mutant of tryptophan 2,3-dioxygenase from xanthomonas campestris”. X-ray diffraction, 2 ligands (TRP, HEM), 20 pockets (best druggability 0.90). MolNFT v1 #58994 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BK9
- Type
- protein
- Length
- 2,120 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan 2,3-dioxygenase
- EC
- 1.13.11.11
- UniProt
- Q8PDA8
- Ligands
- TRP, HEM
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 8 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 277 | 63% helix, 0% strand | Q8PDA8 |
| B | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 280 | 61% helix, 0% strand | Q8PDA8 |
| C | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 272 | 62% helix, 0% strand | Q8PDA8 |
| D | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 262 | 66% helix, 0% strand | Q8PDA8 |
| E | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 260 | 66% helix, 0% strand | Q8PDA8 |
| F | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 250 | 67% helix, 0% strand | Q8PDA8 |
| G | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 262 | 66% helix, 0% strand | Q8PDA8 |
| H | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 257 | 67% helix, 0% strand | Q8PDA8 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 13 copies · chains A, B, C, D, E, F, G, H
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.90 | 0.93 | 126 | TRP |
| 2 | 460 | 0.87 | 0.94 | 49 | TRP, HEM |
| 3 | 505 | 0.87 | 0.94 | 55 | TRP, HEM |
| 4 | 594 | 0.87 | 0.92 | 72 | TRP |
| 5 | 468 | 0.87 | 0.93 | 49 | TRP, HEM |
Interfaces
16 interfaces between chains.
- A–B · 4590 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 3767 Ų buried · 56 hydrogen bonds · protein-protein
- G–H · 3023 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 2891 Ų buried · 52 hydrogen bonds · protein-protein
- E–H · 1551 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3BK9 · H55A mutant of tryptophan 2,3-dioxygenase from Xanthomonas campestris · the same entry in another collection · chain G against G, 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 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 Q8PDA8
- Elsewhere: RCSB PDB 3BK9 · PDBe 3BK9 · UniProt Q8PDA8
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