MolNFT v1 · #119339 · protein
Crystal structure of the cysteine desulfurase csda (persulfurated) from escherichia COLI at 2.384 angstroem resolution
5FT5 · L-cysteine desulfurase csda: “Crystal structure of the cysteine desulfurase csda (persulfurated) from escherichia COLI at 2.384 angstroem…”. X-ray diffraction, 1 ligand (PLP), 6 pockets (best druggability 0.75). MolNFT v1 #119339 on…
- PDB
- 5FT5
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-cysteine desulfurase csda
- EC
- 2.8.1.7, 4.4.1.-, 4.4.1.16
- UniProt
- Q46925
- Ligands
- PLP
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-cysteine desulfurase csda (EC 2.8.1.7, 4.4.1.-, 4.4.1.16) | protein | 400 | 42% helix, 17% strand | Q46925 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.75 | 0.83 | 94 | GOL, TLA, PLP |
| 2 | 493 | 0.72 | 0.81 | 79 | TLA, PLP, GOL |
| 3 | 61 | 0.64 | 0.94 | 18 | empty |
| 4 | 183 | 0.59 | 0.81 | 28 | empty |
| 5 | 112 | 0.59 | 0.85 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 3279 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 modified (pyridoxal phosphate Schiff base, oxidation).
Compared structures
- 5FT5 · Crystal structure of the cysteine desulfurase CsdA (persulfurated) from Escherichia coli… · the same entry in another collection · chain A against A, TM-score 1.00
- Q46925 · AlphaFold monomer V2.0 prediction for cysteine desulfurase csda (Q46925) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q46925
- Elsewhere: RCSB PDB 5FT5 · PDBe 5FT5 · UniProt Q46925
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.