MolNFT v1 · #61926 · protein
H55S mutant xanthomonas campestris tryptophan 2,3-dioxygenase
3E08: “H55S mutant xanthomonas campestris tryptophan 2,3-dioxygenase”. X-ray diffraction, 2 ligands (TRP, HEM), 20 pockets (best druggability 0.90). MolNFT v1 #61926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3E08
- Type
- protein
- Length
- 2,227 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 · 4 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 280 | 62% helix, 0% strand | Q8PDA8 |
| E | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 278 | 63% helix, 0% strand | Q8PDA8 |
| F, H | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 276 | 63% helix, 0% strand | Q8PDA8 |
| G | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 277 | 62% helix, 0% strand | Q8PDA8 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 16 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 | 1062 | 0.90 | 0.92 | 120 | TRP |
| 2 | 967 | 0.90 | 0.92 | 110 | TRP |
| 3 | 460 | 0.87 | 0.94 | 55 | TRP, HEM |
| 4 | 466 | 0.87 | 0.94 | 55 | TRP, HEM |
| 5 | 457 | 0.87 | 0.94 | 51 | TRP, HEM |
Interfaces
16 interfaces between chains.
- C–D · 4601 Ų buried · 60 hydrogen bonds · protein-protein
- G–H · 4592 Ų buried · 62 hydrogen bonds · protein-protein
- E–F · 4583 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 4572 Ų buried · 59 hydrogen bonds · protein-protein
- A–D · 1623 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
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 3E08 · PDBe 3E08 · UniProt Q8PDA8
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