MolNFT v1 · #105375 · protein
X-ray structure of the tryptophan lyase nosl with tryptophan and S- adenosyl-L-homocysteine bound
4R33: “X-ray structure of the tryptophan lyase nosl with tryptophan and S- adenosyl-L-homocysteine bound”. X-ray diffraction, 6 ligands (SAH, SF4, TRP), 8 pockets (best druggability 0.86). MolNFT v1 #105375 on GenesisL1: 3D structure…
- PDB
- 4R33
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nosl
- UniProt
- C6FX51
- Ligands
- SAH, SF4, TRP, K, NA, CL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nosl | protein | 384 | 40% helix, 13% strand | C6FX51 |
| B | Nosl | protein | 384 | 40% helix, 12% strand | C6FX51 |
Ligands and binding sites
- 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
- K · Potassium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.86 | 0.96 | 53 | SAH, SF4, TRP |
| 2 | 318 | 0.86 | 0.96 | 52 | SAH, SF4, TRP |
| 3 | 170 | 0.51 | 0.78 | 21 | empty |
| 4 | 93 | 0.42 | 0.79 | 20 | empty |
| 5 | 50 | 0.41 | 0.83 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 666 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4R33 · X-ray structure of the tryptophan lyase NosL with Tryptophan 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 4R33 · PDBe 4R33 · UniProt C6FX51
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