Research workbench
Structural changes during cysteine desulfurase csda and sulfur- acceptor csde interactions provide insight into the trans- persulfuration
Analyse Structural changes during cysteine desulfurase csda and sulfur- acceptor csde… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LW2
- Type
- protein
- Length
- 1,196 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine sulfinate desulfinase
- EC
- 4.4.1.-
- UniProt
- Q46925
- Ligands
- PLP
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cysteine sulfinate desulfinase (EC 4.4.1.-) | protein | 399 | 43% helix, 17% strand | Q46925 |
| C | Cysteine sulfinate desulfinase (EC 4.4.1.-) | protein | 398 | 43% helix, 17% strand | Q46925 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.73 | 0.81 | 87 | PLP, GOL |
| 2 | 485 | 0.71 | 0.81 | 78 | PLP, GOL |
| 3 | 564 | 0.66 | 0.77 | 59 | empty |
| 4 | 200 | 0.61 | 0.82 | 29 | empty |
| 5 | 103 | 0.56 | 0.85 | 27 | empty |
Interfaces
2 interfaces between chains.
- B–C · 3271 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 161 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4LW2 · Structural changes during cysteine desulfurase CsdA and sulfur-acceptor CsdE interactions… · 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 C 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 4LW2 · PDBe 4LW2 · UniProt Q46925
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