Research workbench
Tryptophan lyase 'empty state'
Analyse Tryptophan lyase 'empty state' in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HTO
- Type
- protein
- Length
- 759 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Streptomyces actuosus
- Molecule
- 3-methyl-2-indolic acid synthase
- UniProt
- C6FX51
- Ligands
- SF4, MET, 5AD, CL
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · resolution 1.45 · 2 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-methyl-2-indolic acid synthase | protein | 380 | 40% helix, 12% strand | C6FX51 |
| B | 3-methyl-2-indolic acid synthase | protein | 379 | 40% helix, 13% strand | C6FX51 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- MET · Methionine · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 11 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.86 | 0.97 | 47 | SF4, MET, 5AD, CL |
| 2 | 290 | 0.86 | 0.96 | 52 | SF4, MET, 5AD, CL |
| 3 | 54 | 0.33 | 0.78 | 14 | GOL |
| 4 | 59 | 0.32 | 0.77 | 16 | GOL |
| 5 | 81 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1095 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6HTO · Tryptophan lyase 'empty state' · the same entry in another collection · 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 C6FX51
- Elsewhere: RCSB PDB 6HTO · PDBe 6HTO · UniProt C6FX51
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