Research workbench
Crystal structure of the cysteine desulfurase csda (S-sulfonic acid) from escherichia COLI at 2.050 angstroem resolution
Analyse Crystal structure of the cysteine desulfurase csda (S-sulfonic acid) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FT6
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase csda
- EC
- 2.8.1.7, 4.4.1.-, 4.4.1.16
- UniProt
- Q46925
- Ligands
- PLP
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase csda (EC 2.8.1.7, 4.4.1.-, 4.4.1.16) | protein | 400 | 41% helix, 16% strand | Q46925 |
| B | Cysteine desulfurase csda (EC 2.8.1.7, 4.4.1.-, 4.4.1.16) | protein | 399 | 43% helix, 17% strand | Q46925 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 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 | 633 | 0.78 | 0.84 | 99 | PLP, GOL |
| 2 | 490 | 0.72 | 0.82 | 71 | GOL, PLP |
| 3 | 243 | 0.63 | 0.81 | 30 | empty |
| 4 | 74 | 0.43 | 0.80 | 19 | empty |
| 5 | 68 | 0.33 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3281 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 modified (pyridoxal phosphate Schiff base, nonstandard).
Compared structures
- 5FT6 · Crystal structure of the cysteine desulfurase CsdA (S-sulfonic acid) from Escherichia… · 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 5FT6 · PDBe 5FT6 · UniProt Q46925
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