Research workbench
Crystal structure of the cysteine desulfurase csda (persulfurated) from escherichia COLI at 2.384 angstroem resolution
Analyse Crystal structure of the cysteine desulfurase csda (persulfurated) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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