Research workbench
X-ray structure of the tryptophan lyase NosL with Tryptophan, 5'-deoxyadenosine and methionine bound
Analyse X-ray structure of the tryptophan lyase NosL with Tryptophan, 5'-deoxyadenosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R34
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Streptomyces actuosus
- Molecule
- NosL
- UniProt
- C6FX51
- Ligands
- MET, 5AD, SAH, SF4, TRP, NA, ZN, BR
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NosL | protein | 384 | 41% helix, 14% strand | C6FX51 |
| B | NosL | protein | 384 | 40% helix, 13% strand | C6FX51 |
Ligands and binding sites
- MET · Methionine · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains B
- BR · Bromide ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.86 | 0.96 | 55 | MET, 5AD, SAH, SF4, TRP |
| 2 | 302 | 0.86 | 0.96 | 52 | MET, 5AD, SAH, SF4, TRP |
| 3 | 173 | 0.50 | 0.78 | 27 | empty |
| 4 | 97 | 0.44 | 0.79 | 21 | empty |
| 5 | 52 | 0.38 | 0.81 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 662 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4R34 · X-ray structure of the tryptophan lyase nosl with tryptophan, 5'- deoxyadenosine and… · 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 4R34 · PDBe 4R34 · UniProt C6FX51
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